6WJB
UDP-GlcNAc C4-epimerase from Pseudomonas protegens in complex with NAD and UDP-GlcNAc
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1SB8 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 298 | 0.2 M ammonium sulphate, 0.1 M sodium citrate pH 5.6, 25% (w/v) PEG 4000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.81 | 56.26 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 123.04 | α = 90 |
b = 75.455 | β = 90 |
c = 79.156 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | 2012-07-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | 1.075 | NSLS | X29A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
1 | 2.1 | 50 | 100 | 0.08 | 38.8 | 11.4 | 43495 | 33.4 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.1 | 2.18 | 100 | 0.58 | 5.3 | 14.6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1SB8 | 2.1 | 49.92 | 43027 | 1976 | 98.84 | 0.1682 | 0.1668 | 0.1969 | 41.13 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 14.5855 |
f_angle_d | 0.8813 |
f_chiral_restr | 0.0477 |
f_bond_d | 0.0062 |
f_plane_restr | 0.0046 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4503 |
Nucleic Acid Atoms | |
Solvent Atoms | 217 |
Heterogen Atoms | 140 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
PHENIX | phasing |