6CIA
Crystal structure of aldo-keto reductase from Klebsiella pneumoniae in complex with NADPH.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 289.15 | 0.2 ul of 11 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 Top 96 #90 (0.2 uL 0.1 M Tris: HCl, pH 8.5, 25 % (w/v) PEG 3350) and 0.1 uL 30%v/v Ethanol (Additive Screen #82) 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 |
2.31 | 46.85 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 83.626 | α = 90 |
b = 83.626 | β = 90 |
c = 72.834 | γ = 120 |
Symmetry | |
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Space Group | P 32 2 1 |
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 300 mm CCD | mirrors | 2017-04-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97856 | APS | 21-ID-G |
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) | CC (Half) | 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 | 2.3 | 50 | 100 | 0.083 | 0.083 | 0.088 | 0.03 | 1 | 30.9 | 8.3 | 13360 | -3 | 33.7 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||
1 | 2.3 | 2.34 | 100 | 1.092 | 1.092 | 1.178 | 0.438 | 0.838 | 1.9 | 7 |
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 | 4WGH | 2.3 | 50 | 11434 | 612 | 89.94 | 0.17052 | 0.16727 | 0.22957 | RANDOM | 43.872 |
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] | |
-0.35 | -0.18 | -0.35 | 1.14 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.689 |
r_dihedral_angle_4_deg | 15.979 |
r_dihedral_angle_3_deg | 13.35 |
r_long_range_B_refined | 6.399 |
r_long_range_B_other | 6.3 |
r_dihedral_angle_1_deg | 5.879 |
r_scangle_other | 4.423 |
r_scbond_it | 3.005 |
r_scbond_other | 2.97 |
r_mcangle_it | 2.605 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2215 |
Nucleic Acid Atoms | |
Solvent Atoms | 150 |
Heterogen Atoms | 48 |
Software
Software | |
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Software Name | Purpose |
MD2 | data collection |
HKL-3000 | data scaling |
SCALEPACK | data scaling |
HKL-3000 | data reduction |
HKL-3000 | phasing |
MOLREP | phasing |
REFMAC | refinement |