1HO4
CRYSTAL STRUCTURE OF PYRIDOXINE 5'-PHOSPHATE SYNTHASE IN COMPLEX WITH PYRIDOXINE 5'-PHOSPHATE AND INORGANIC PHOSPHATE
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1HO1 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293 | 10% PEG6000, 2M NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 20K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.05 | 59.68 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 128.8 | α = 90 |
b = 156.3 | β = 90 |
c = 127.5 | 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 | IMAGE PLATE | MARRESEARCH | 2000-01-31 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU300 | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 25 | 96.2 | 0.046 | 0.046 | 8.6 | 2 | 54860 | 110743 | 38.8 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.3 | 2.4 | 95.7 | 0.208 | 0.208 | 3.6 | 2.4 | 13071 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | PDB entry 1HOI | 2.3 | 20 | 54828 | 52092 | 2736 | 0.195 | 0.195 | 0.187 | 0.245 | random | 56.6 |
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 |
c_mcbond_it | 2.33 |
c_angle_deg | 1.54 |
n_bond_d | 0.011 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7334 |
Nucleic Acid Atoms | |
Solvent Atoms | 735 |
Heterogen Atoms | 79 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
DENZO | data reduction |
CCP4 | data scaling |