Statistics Summary Report for BIGS Center

Last updated: Mar 11 2010

• Target Status Statistics
  • Table 1: Status Statistics for BIGS
  • Table 2: Status Statistics for BIGS by Organisms
• Deposited Structure Statistics
  • Table 3: PDB Status Statistics for Structures from BIGS
  • Table 4: List of Structures Deposited by BIGS in the PDB
• Sequence Redundancy Statistics
  • Table 5: Sequence Redundancy Statistics for BIGS by Experimental Status
  • Table 6: Sequence Redundancy Statistics for Structures Released by BIGS in the PDB by Year

Target Status Statistics

Total number of targets deposited by BIGS to TargetDB: 297

      View BIGS Target List

Table 1: Status Statistics for BIGS

Status	Total Number of Targets	(%) Relative to "Cloned" Targets	(%) Relative to "Expressed" Targets	(%) Relative to "Purified" Targets	(%) Relative to "Crystallized" Targets
Cloned	251	100.0	-	-	-
Expressed	223	88.8	100.0	-	-
Soluble	151	60.2	67.7	-	-
Purified	110	43.8	49.3	100.0	-
Crystallized	28	11.2	12.6	25.5	100.0
Diffraction-quality Crystals	21	8.4	9.4	19.1	75.0
Diffraction	19	7.6	8.5	17.3	67.9
NMR Assigned	0	0.0	0.0	0.0	-
HSQC	0	0.0	0.0	0.0	-
Crystal Structure	17	6.8	7.6	15.5	60.7
NMR Structure	0	0.0	0.0	0.0	-
In PDB1	9	3.6	4.0	8.2	32
Work Stopped	3	-	-	-	-
Test Target	1	-	-	-	-
Other	0	-	-	-	-

Last updated: Mar 11 2010

Table 2: Status Statistics for BIGS by Organism

These statistics are derived from mapping of target sequences to GenBank using >=98% sequence identity cut off

Organism	Total Number1	Work Stopped	Cloned	Expressed	Purified	Crystallized	Crystal Structure	NMR Structure	In PDB2
Viruses	1	0	1	1	0	0	0	0	0
Bacteria	186	3	167	146	74	18	11	0	8
Prokaryota	186	3	167	146	74	18	11	0	8
Yeast	57	0	53	52	23	5	2	0	0
Eukaryota	110	0	83	76	35	10	6	0	1
Uncultured or unidentified	2	0	2	1	0	0	0	0	0

Last updated: Mar 11 2010

Note 1:   Total counts in this table may differ from total number of targets and structures. A target is counted in different organism specifications if:
- a target is mapped to different organisms
- a targtet is a hybrid complex (for example:a complex of human and mouse polypeptides)

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Deposited Structure Statistics for BIGS Center

Number of Released X-Ray Structures: 8

Number of Released NMR Structures: 0

Total number of released structures from BIGS center in the PDB: 8

Table 3: PDB Status Statistics for Structures from BIGS

PDB Status	Number of Structures
Total Deposited	9
Released	8
Release on Publication	0
Release on Certain Date	0
In Process	1

Last updated: Mar 11 2010

Note 1:   "Total Deposited" are all structures in the PDB including structures released to the public and structures that are in the process to be released("Released on Publication" , "Released on Certain Date", etc.).

Table 4: List of Structures Deposited in the PDB by BIGS

Total number of structures: 9

Structures of distinct targets: 91

1   A target may reference several PDB IDs (example: structure of the same polypeptides with different ligands).
In this case only one structure is counted to compute number of structures of distinct targets

Related PDB_ID(s): PDB_ID(s) associated with the same target in targetDB

PDB_ID	Title	Target_id	Deposition Date	Released Date	PDB Status	Related PDB_ID in TargetDB
ND_135	Experimental status "in PDB", PDB ID is not provided	Pf-cal:CA1462	-	-	-	none
1UUF	crystal structure of a zinc-type alcohol dehydrogenase-like protein yahk	ASG-yahK	2003-12-18	2004-01-29	REL	none
1OG6	ydhf, an aldo-keto reductase from e.coli complexed with nadph	ASG-ydhF	2003-04-24	2003-05-29	REL	none
1J2R	crystal structure of escherichia coli gene product yecd at 1.3 a resolution	ASG-yecD	2003-01-09	2004-01-27	REL	none
1OKJ	mad crystal structure of the unknown function e. coli yeaz protein	IGS-yeaZ	2003-07-26	2004-09-16	REL	none
1GPQ	structure of ivy complexed with its target, hewl	ORPH-ykfE	2001-11-08	2003-03-11	REL	none
1OI4	cristal structure of yhbo from escherichia coli	ASG-yhbO	2003-06-06	2003-07-03	REL	none
1UQW	crystal structure of ylib protein from escherichia coi	ASG-yliB	2003-10-22	2003-10-22	REL	none
1MZR	structure of dkga from e.coli at 2.13 a resolution solved by molecular replacement	ASG-yqhE	2002-10-09	2003-10-28	REL	none

Note 1:  Last updated: Mar 11 2010

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Sequence Redundancy Statistics

Table 5: Sequence Redundancy Statistics for BIGS by Experimental Status

Sequence Identity(%)	Novel Targets Status: Selected	Novel Targets Status: Cloned	Novel Targets Status: Expressed	Novel Targets Status: Purified	Novel Targets Status: Crystallized	Novel Targets Status: Crystal Structure	Novel Targets Status: in PDB
<100	297	251	223	110	28	17	9
<90	296	250	222	110	28	17	9
<70	289	249	221	110	28	17	9
<50	282	245	218	110	28	17	9
<30	228	210	191	98	27	17	9

Last updated: 10-03-08

Sequence redundancy is calculated by clustering analysis using BLASTClust program with similarity threshold set to percent of sequence identity.   Please view detailed explanation of sequence redundancy calculations and BLASTClust threshold settings.  Sequence redundancy calculations are based on comparison to all protein sequences in TargetDB which are in the same experimental status category and at least 20 amino acids long

Table 6:Sequence Redundancy Statistics for Structures Released by BIGS by Year

Year	Released Structures	Number of Released Structures <30% Identity at Time of Release	Percent(%) of Released Structures <30% Identity(%) at Time of Release
2003	5	3	60
2004	3	1	33
Total	8	4	50

Last updated:10-03-11

Sequence redundancy is calculated by clustering analysis using BLASTClust program with similarity threshold set to percent of sequence identity.   Please view detailed explanation of sequence redundancy calculations and BLASTClust threshold settings.  Sequence redundancy calculations are based on comparison to all protein sequences in the PDB which are at least 20 amino acids long

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