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Crystal structure of aldo/keto reductase from Klebsiella pneumoniae in complex with NADP and acetate at 1.8 A resolution
Crystallization Crystalization Experiments 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 Matthews coefficient Solvent content 2.3 46.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.483 α = 90 b = 99.483 β = 90 c = 55.181 γ = 120
Diffraction Diffraction Experiment 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 ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall 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 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 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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.8 50 27524 1473 99.87 0.1466 0.1446 0.1452 0.1854 0.1845 RANDOM 38.07
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] -1.17 -0.59 -1.17 3.8
RMS Deviations 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
RMS Deviations 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 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2166 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 52
Software Software 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