5VMT
Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae bound to NAD
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 289 | NegoA.00617.a.B1.PS38018 at 21.2 mg/mL with 3 mM NAD against JCSG+ screen condition A9 0.2 M ammonium chloride, 25% PEG 3350 supplemented with 20% ethylene glycol and 3 mM NAD as cryoprotectant, crystal tracking ID 284230a9, unique puck ID giy4-10 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.48 | 50.46 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 142.45 | α = 90 |
b = 132.1 | β = 94.56 |
c = 156 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 | MARMOSAIC 300 mm CCD | 2016-11-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | 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 | 2.5 | 45.485 | 99.8 | 0.066 | 0.077 | 0.998 | 15.53 | 3.816 | 99272 | -3 | 41.89 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.5 | 2.56 | 100 | 0.491 | 0.57 | 0.822 | 2.84 | 3.862 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | NONE | 4QX6 | 2.5 | 45.485 | 1.35 | 99255 | 1994 | 99.79 | 0.1661 | 0.165 | 0.219 | 53.9116 |
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 | 13.531 |
f_angle_d | 0.936 |
f_chiral_restr | 0.057 |
f_bond_d | 0.007 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 19016 |
Nucleic Acid Atoms | |
Solvent Atoms | 646 |
Heterogen Atoms | 358 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
MOLREP | phasing |