2PZM
Crystal structure of the Bordetella bronchiseptica enzyme WbmG in complex with NAD and UDP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2PZK | PDB ENTRY 2PZK |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293 | 0.1 M Hepes, 1.6 M (NH4)2SO4, 2 % (v/v) PEG 400, 10 mM UDP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.67 | 53.85 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 58.214 | α = 90 |
b = 140.481 | β = 90 |
c = 184.139 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
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 | 2006-05-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | 0.977 | ESRF | ID14-4 |
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 | 30 | 99.9 | 0.085 | 19.6 | 5.9 | 51224 | 51158 | 2 |
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 | 2.03 | 100 | 0.773 | 2.28 | 5.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2PZK | 2 | 30 | 51224 | 51115 | 2591 | 99.68 | 0.1708 | 0.1708 | 0.221 | RANDOM | 28.315 |
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] | |
2.65 | -1.3 | -1.35 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.944 |
r_dihedral_angle_3_deg | 14.805 |
r_dihedral_angle_4_deg | 14.188 |
r_dihedral_angle_1_deg | 8.305 |
r_scangle_it | 2.651 |
r_scbond_it | 1.867 |
r_angle_refined_deg | 1.7 |
r_mcangle_it | 1.175 |
r_mcbond_it | 0.75 |
r_nbtor_refined | 0.305 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4685 |
Nucleic Acid Atoms | |
Solvent Atoms | 473 |
Heterogen Atoms | 136 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
ADSC | data collection |
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |