- PDB-3gyd: Crystal structure of a cyclic nucleotide-binding domain (mfla_192... -
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Basic information
Entry
Database: PDB / ID: 3gyd
Title
Crystal structure of a cyclic nucleotide-binding domain (mfla_1926) from methylobacillus flagellatus kt at 1.79 A resolution
Components
Cyclic nucleotide-binding domain
Keywords
DNA BINDING PROTEIN / Nucleotide binding protein / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Resolution: 1.79→29.374 Å / Num. obs: 30961 / % possible obs: 99.1 % / Redundancy: 3 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 6.144
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
1.79-1.84
2.3
0.559
1.1
4786
2066
0.559
90.8
1.84-1.89
2.7
0.547
1.2
6128
2230
0.547
98
1.89-1.94
3.1
0.473
1.4
6675
2141
0.473
100
1.94-2
3.1
0.366
1.8
6615
2120
0.366
100
2-2.07
3.1
0.271
2.5
6358
2034
0.271
100
2.07-2.14
3.1
0.221
3
6230
2008
0.221
100
2.14-2.22
3.1
0.194
3.5
5947
1896
0.194
100
2.22-2.31
3.1
0.16
4.1
5829
1864
0.16
100
2.31-2.41
3.1
0.132
5
5475
1749
0.132
100
2.41-2.53
3.1
0.126
5.3
5285
1694
0.126
100
2.53-2.67
3.1
0.108
6.3
5099
1626
0.108
100
2.67-2.83
3.1
0.092
7.4
4787
1528
0.092
100
2.83-3.03
3.1
0.083
7.9
4519
1444
0.083
100
3.03-3.27
3.1
0.074
8.6
4173
1342
0.074
99.8
3.27-3.58
3.1
0.066
9.4
3815
1237
0.066
99.9
3.58-4
3.1
0.054
11.1
3531
1135
0.054
99.8
4-4.62
3.1
0.048
13
3050
982
0.048
99.6
4.62-5.66
3.1
0.048
12.9
2603
838
0.048
99.4
5.66-8.01
3
0.056
10.8
1997
659
0.056
98.9
8.01-29.374
2.9
0.041
15.2
1070
368
0.041
96
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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
MAR345
CCD
datacollection
MOSFLM
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.79→29.374 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 5.717 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.128 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. AN ADENOSINE-3'-5'-CYCLIC-MONOPHOSPHATE (CMP) IS MODELED INTO THE LIGAND BINDING SITE ON EACH MONOMER BASED ON THE PRESENCE OF CLEAR AND CONCLUSIVE ELECTRON DENSITY.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.212
1549
5 %
RANDOM
Rwork
0.168
-
-
-
obs
0.17
30921
98.82 %
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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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