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Crystal structure of aldo-keto reductase from Klebsiella pneumoniae in complex with NADPH.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WGH
Crystallization Crystalization Experiments 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 Matthews coefficient Solvent content 2.31 46.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.626 α = 90 b = 83.626 β = 90 c = 72.834 γ = 120
Symmetry Space Group P 32 2 1
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 300 mm CCD mirrors 2017-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall 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 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 4WGH 2.3 50 11434 612 89.94 0.17052 0.16727 0.1733 0.22957 0.2282 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 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
RMS Deviations 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 r_mcangle_other 2.605 r_mcbond_it 1.749 r_mcbond_other 1.735 r_angle_refined_deg 1.363 r_angle_other_deg 0.968 r_chiral_restr 0.071 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2215 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 48
Software Software Software Name Purpose MD2 data collection HKL-3000 data scaling SCALEPACK data scaling HKL-3000 data reduction HKL-3000 phasing MOLREP phasing REFMAC refinement