5ZWB
Crystal structure of Pyridoxal kinase (PdxK) from Salmonella typhimurium in complex with ADP, PL-linked to Lys233 via a Schiff base
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2DDM |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | BATCH MODE | 8.5 | 293 | 50% PEG 4000, 10% Glycerol, 100mM Tris |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.61 | 51.77 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 73.7 | α = 90 |
b = 73.7 | β = 90 |
c = 248.31 | γ = 90 |
Symmetry | |
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Space Group | P 43 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 | MARMOSAIC 225 mm CCD | 2013-01-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM14 | 0.97625 | ESRF | BM14 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 2.2 | 39.94 | 100 | 0.11 | 0.12 | 0.03 | 15.5 | 14.4 | 36036 | 28 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.2 | 2.32 | 100 | 0.45 | 0.46 | 0.11 | 5.8 | 15.3 |
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 | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2DDM | 2.2 | 39.9 | 34098 | 1766 | 99.95 | 0.21175 | 0.21023 | 0.24226 | RANDOM | 33.055 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
1.49 | 1.49 | -2.98 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.196 |
r_dihedral_angle_4_deg | 15.46 |
r_dihedral_angle_3_deg | 11.598 |
r_dihedral_angle_1_deg | 4.649 |
r_long_range_B_refined | 3.784 |
r_long_range_B_other | 3.716 |
r_mcangle_it | 1.344 |
r_mcangle_other | 1.344 |
r_scangle_other | 1.081 |
r_angle_refined_deg | 0.883 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4055 |
Nucleic Acid Atoms | |
Solvent Atoms | 328 |
Heterogen Atoms | 105 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
iMOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |