- PDB-3fj2: CRYSTAL STRUCTURE OF A MONOOXYGENASE-LIKE PROTEIN (LIN2316) FROM ... -
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Basic information
Entry
Database: PDB / ID: 3fj2
Title
CRYSTAL STRUCTURE OF A MONOOXYGENASE-LIKE PROTEIN (LIN2316) FROM LISTERIA INNOCUA AT 1.85 A RESOLUTION
Components
Monooxygenase-like Protein
Keywords
UNKNOWN FUNCTION / MONOOXYGENASE-LIKE PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Resolution: 1.85→28.88 Å / Num. obs: 29746 / % possible obs: 99.9 % / Redundancy: 14 % / Biso Wilson estimate: 20.997 Å2 / Rmerge(I) obs: 0.161 / Rsym value: 0.161 / Net I/σ(I): 2.986
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
1.85-1.9
14.4
0.947
0.8
30636
2124
0.947
99.8
1.9-1.95
14.4
0.785
0.8
29950
2086
0.785
99.8
1.95-2.01
14.4
0.623
1.2
29208
2032
0.623
99.9
2.01-2.07
14.4
0.508
1.3
28423
1977
0.508
99.9
2.07-2.14
14.4
0.444
1.5
27613
1922
0.444
99.9
2.14-2.21
14.4
0.36
2.1
26872
1869
0.36
100
2.21-2.29
14.2
0.326
1
25558
1797
0.326
100
2.29-2.39
14.3
0.284
2.6
24794
1730
0.284
100
2.39-2.49
14.2
0.241
3
23792
1670
0.241
100
2.49-2.62
14.2
0.211
3.4
22897
1612
0.211
100
2.62-2.76
14.1
0.173
3.8
21825
1545
0.173
100
2.76-2.93
14
0.152
4.4
20443
1456
0.152
100
2.93-3.13
13.9
0.133
4.8
18948
1368
0.133
100
3.13-3.38
13.5
0.124
5
17668
1304
0.124
100
3.38-3.7
13.4
0.105
5.5
16089
1201
0.105
100
3.7-4.14
13.3
0.097
5.8
14547
1097
0.097
100
4.14-4.78
13.1
0.09
6.2
12919
989
0.09
100
4.78-5.85
12.8
0.099
5.5
10828
847
0.099
100
5.85-8.27
12.3
0.105
3.9
8565
695
0.105
100
8.27-28.88
10.5
0.089
5.3
4465
425
0.089
97.6
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0019
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
SCALA
3.2.5
datascaling
PDB_EXTRACT
3.006
dataextraction
MOSFLM
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.85→28.88 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 3.76 / SU ML: 0.058 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.087 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. GLYCEROL (GOL) MOLECULES FROM CRYO SOLUTION ARE MODELED.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.186
1504
5.1 %
RANDOM
Rwork
0.167
-
-
-
obs
0.168
29683
99.84 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
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