- PDB-1tt7: Crystal structure of Bacillus subtilis protein yhfP -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 1tt7
Title
Crystal structure of Bacillus subtilis protein yhfP
Components
YHFP
Keywords
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / yhfp / alcohol dehydrogenase / Zn-dependent / NAD / Protein Structure Initiative / PSI / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information
acryloyl-CoA reductase (NADPH) activity / Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor / cytoplasm Similarity search - Function
Resolution: 2.7→20 Å / Rmerge(I) obs: 0.128 / Num. unique all: 7 / % possible all: 99.1
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Processing
Software
Name
Version
Classification
REFMAC
5.2.0003
refinement
DENZO
datareduction
SCALEPACK
datascaling
SOLVE
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.872 / SU B: 27.422 / SU ML: 0.252 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.26192
3148
5.1 %
RANDOM
Rwork
0.18729
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all
0.19111
61904
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obs
0.19111
58764
98.71 %
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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
Displacement parameters
Biso mean: 29.932 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.76 Å2
0 Å2
0 Å2
2-
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3.03 Å2
0 Å2
3-
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-3.8 Å2
Refinement step
Cycle: LAST / Resolution: 2.7→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
14617
0
0
160
14777
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.035
0.022
14833
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
3.006
1.973
20132
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
8.293
5
1968
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
44.097
25.053
570
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
21.57
15
2496
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.491
15
78
X-RAY DIFFRACTION
r_chiral_restr
0.189
0.2
2358
X-RAY DIFFRACTION
r_gen_planes_refined
0.01
0.02
11038
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.313
0.2
8318
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.354
0.2
10288
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.24
0.2
742
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.25
0.2
38
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.184
0.2
2
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_mcbond_it
3.19
1.5
9946
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
5.064
2
15536
X-RAY DIFFRACTION
r_scbond_it
4.55
3
5570
X-RAY DIFFRACTION
r_scangle_it
6.901
4.5
4596
X-RAY DIFFRACTION
r_rigid_bond_restr
3.536
3
15516
X-RAY DIFFRACTION
r_sphericity_free
14.127
3
160
X-RAY DIFFRACTION
r_sphericity_bonded
4.478
3
14617
LS refinement shell
Highest resolution: 2.7 Å / Num. reflection Rwork: 4021 / Total num. of bins used: 20
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