6KIY

Crystal structure of a thermostable aldo-keto reductase Tm1743 in complex with inhibitor Epalrestat


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5DAN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP428910% Jeffamine M600, 0.1 M sodium acetate trihydrate
Crystal Properties
Matthews coefficientSolvent content
3.0359.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.172α = 90
b = 84.172β = 90
c = 93.166γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-11-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL18U10.97861SSRFBL18U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.972.91000.1640.0384.519.230676
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.931000.750.1784.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5DAN1.942.1229156148899.90.17340.17190.2025RANDOM20.579
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]
0.340.170.34-1.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.845
r_dihedral_angle_4_deg12.747
r_dihedral_angle_3_deg11.766
r_dihedral_angle_1_deg5.763
r_angle_refined_deg1.467
r_angle_other_deg0.443
r_chiral_restr0.062
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.845
r_dihedral_angle_4_deg12.747
r_dihedral_angle_3_deg11.766
r_dihedral_angle_1_deg5.763
r_angle_refined_deg1.467
r_angle_other_deg0.443
r_chiral_restr0.062
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2212
Nucleic Acid Atoms
Solvent Atoms92
Heterogen Atoms61

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
Cootmodel building
PHASERphasing
HKL-3000data reduction
HKL-3000data scaling