BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.
Remark 999
SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
Resolution: 2.11→47.836 Å / Num. obs: 102365 / % possible obs: 98.1 % / Redundancy: 3.8 % / Biso Wilson estimate: 30.01 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 8.2
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
2.11-2.22
3.8
0.584
1.3
56494
15031
0.584
99.4
2.22-2.36
3.8
0.424
1.8
53291
14138
0.424
99.1
2.36-2.52
3.8
0.33
2.3
50358
13308
0.33
98.9
2.52-2.72
3.8
0.228
3.4
47014
12389
0.228
98.6
2.72-2.98
3.8
0.149
5.2
43260
11359
0.149
98.3
2.98-3.34
3.8
0.084
9
39169
10243
0.084
97.8
3.34-3.85
3.8
0.051
14.1
34696
9055
0.051
97.4
3.85-4.72
3.8
0.034
19.4
29374
7645
0.034
96.7
4.72-6.67
3.8
0.034
18.2
22497
5906
0.034
95.8
6.67-47.836
3.7
0.025
20.9
12067
3291
0.025
93.5
-
Phasing
Phasing
Method: MAD
-
Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0019
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
SCALA
datascaling
PDB_EXTRACT
2
dataextraction
MAR345
CCD
datacollection
XDS
datareduction
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.11→47.836 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.942 / SU B: 11.373 / SU ML: 0.148 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.151 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. SO4, GOL, IPA WERE MODELED BASED ON CRYSTALLIZATION/CRYO CONDITION. 5. THE ACTIVE SITE IS FORMED BY FOLLOWING LOOPS: 22-30, 75-117, 143-149, 456-467. ALL THESE LOOPS-CONTAINING SITE WAS BUILT BASED ON SIMILARITY TO A STRUCTURE HOMOLOG (1LFW). LOOP 71-117 MAY CONTAIN REGISTER ERRORS. ADDITIONALLY, N-TERMINAL DENSITY IS ALSO POOR. 6. TWO ZINC IONS IN THE ACTIVE SITE WERE MODELED BASED ON HOMOLOGS. X-RAY FLUORESCENCE MEASUREMENTS AND ANOMALOUS DIFFERENCE FOURIERS SUGGEST THAT METAL AT SITE 501 MIGHT BE A MIXTURE OF ZINC AND NICKEL, WHILE THE METAL AT SITE 502 IS MOSTLY ZINC. 7. RAMACHANDRAN OUTLIERS (A26, B293) ARE LOCATED IN REGIONS WITH POOR ELECTRON DENSITY. THE CIS-PEPTIDE 115-116, LOCATED NEAR THE ACTIVE SITE, IS LIKELY VALID.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.244
5107
5 %
RANDOM
Rwork
0.22
-
-
-
all
0.221
-
-
-
obs
0.221
102314
97.68 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
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