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Aldo-keto reductase KmAKR - W297H
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 Sodium acetate trihydrate,TRIS hydrochloride,PEG 4000,glycerol
Crystal Properties Matthews coefficient Solvent content 2.13 42.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.453 α = 90 b = 48.031 β = 104.01 c = 66.468 γ = 90
Symmetry Space Group C 1 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 PIXEL DECTRIS EIGER X 9M 2022-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.9792 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.13 64.49 100 0.105 0.114 0.044 0.996 11.3 6.8 16912
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 2.13 2.17 100 0.343 0.373 0.145 0.897 2 6.6
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 AlphaFold 2.13 64.49 16033 878 99.96 0.21498 0.2125 0.2164 0.25973 0.2623 RANDOM 37.104
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] -0.95 0.19 3.42 -2.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.108 r_dihedral_angle_2_deg 10.845 r_dihedral_angle_1_deg 6.397 r_long_range_B_refined 6.246 r_long_range_B_other 6.244 r_scangle_other 5.073 r_mcangle_it 3.947 r_mcangle_other 3.946 r_scbond_it 3.246 r_scbond_other 3.245
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.108 r_dihedral_angle_2_deg 10.845 r_dihedral_angle_1_deg 6.397 r_long_range_B_refined 6.246 r_long_range_B_other 6.244 r_scangle_other 5.073 r_mcangle_it 3.947 r_mcangle_other 3.946 r_scbond_it 3.246 r_scbond_other 3.245 r_mcbond_it 2.719 r_mcbond_other 2.716 r_angle_refined_deg 1.337 r_angle_other_deg 0.422 r_chiral_restr 0.063 r_gen_planes_refined 0.009 r_bond_refined_d 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 2476 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms
Software Software Software Name Purpose DIALS data scaling REFMAC refinement DIALS data reduction MOLREP phasing