4WGH
Crystal structure of aldo/keto reductase from Klebsiella pneumoniae in complex with NADP and acetate at 1.8 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.2 | 289 | 0.45 ul of 13 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide, 0.5 mM TCEP and 30mM NADP were mixed with 0.45 ul of 2.8 M Sodium Acetate pH 6.2 and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.3 | 46.55 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 99.483 | α = 90 |
b = 99.483 | β = 90 |
c = 55.181 | γ = 120 |
Symmetry | |
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Space Group | P 62 |
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 | Beryllium Lenses | 2014-03-20 | 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) | 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 | 1.8 | 50 | 99.1 | 0.048 | 0.056 | 0.028 | 10.2 | 3.9 | 56317 | -3 | 28.4 |
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 | 1.8 | 1.83 | 97.3 | 0.62 | 0.723 | 0.369 | 0.726 | 1.43 | 3.7 | 2809 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 1.8 | 50 | 27524 | 1473 | 99.87 | 0.1466 | 0.1446 | 0.1854 | RANDOM | 38.07 |
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] | |
-1.17 | -0.59 | -1.17 | 3.8 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.649 |
r_dihedral_angle_4_deg | 17.887 |
r_dihedral_angle_3_deg | 14.033 |
r_dihedral_angle_1_deg | 5.831 |
r_angle_refined_deg | 1.654 |
r_mcangle_it | 1.51 |
r_mcbond_it | 1.02 |
r_mcbond_other | 1.012 |
r_angle_other_deg | 0.846 |
r_chiral_restr | 0.092 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2166 |
Nucleic Acid Atoms | |
Solvent Atoms | 227 |
Heterogen Atoms | 52 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
HKL-3000 | data collection |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
HKL-3000 | phasing |
DM | phasing |
MLPHARE | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
DENZO | data reduction |
SCALEPACK | data scaling |