4XK2
Crystal structure of aldo-keto reductase from Polaromonas sp. JS666
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4JTD |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 289 | 0.2 ul of 12 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG Suite 3 condition #81 (0.2M NaCl, 0.1M Na citrate, 40%v/v 1,2-propanodiol pH=5.5) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/50 v/v of 2 mg/ml chymotrypsin solution at 289 K for 3 hours. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.95 | 58.31 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 105.11 | α = 90 |
b = 105.11 | β = 90 |
c = 479.569 | γ = 90 |
Symmetry | |
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Space Group | I 4 2 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 315r | 2014-07-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.979 | APS | 19-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 1.9 | 50 | 100 | 0.082 | 0.082 | 0.09 | 0.036 | 5.8 | 5.9 | 106320 | 106320 | -3 | 27.3 |
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) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.9 | 1.93 | 100 | 0.83 | 0.91 | 0.373 | 0.702 | 1.9 | 5.8 | 5256 |
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 4JTD | 1.9 | 50 | 100839 | 5293 | 99.93 | 0.1617 | 0.1605 | 0.17 | 0.1847 | 0.19 | RANDOM | 45.569 |
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] | |
0.19 | 0.19 | -0.38 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.188 |
r_dihedral_angle_4_deg | 17.86 |
r_dihedral_angle_3_deg | 12.719 |
r_dihedral_angle_1_deg | 5.003 |
r_angle_other_deg | 2.269 |
r_mcangle_it | 2.14 |
r_mcbond_it | 1.329 |
r_mcbond_other | 1.329 |
r_angle_refined_deg | 1.261 |
r_chiral_restr | 0.071 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7159 |
Nucleic Acid Atoms | |
Solvent Atoms | 964 |
Heterogen Atoms | 8 |
Software
Software | |
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Software Name | Purpose |
HKL-3000 | data collection |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
HKL-3000 | phasing |
MOLREP | phasing |
Coot | model building |
REFMAC | refinement |
PDB_EXTRACT | data extraction |