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Aldo-keto reductase KmAKR-W297H/Y296W
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,Polyethylene glycol 4000, glycerol
Crystal Properties Matthews coefficient Solvent content 2.36 47.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.561 α = 90 b = 64.796 β = 105.54 c = 99.793 γ = 90
Symmetry Space Group I 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 0.97918 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 1.5 53.73 100 0.095 0.103 0.04 0.996 11.6 6.7 52646
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 1.5 1.53 100 0.35 0.387 0.16 0.881 2 5.7
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 AlphaFold 1.5 53.73 50056 2587 99.99 0.15396 0.15259 0.1525 0.1809 0.1811 RANDOM 15.97
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] -0.03 0.22 -0.11 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 13.757 r_dihedral_angle_3_deg 13.352 r_long_range_B_refined 6.272 r_dihedral_angle_1_deg 6.2 r_long_range_B_other 6.107 r_scangle_other 5.469 r_scbond_it 3.504 r_scbond_other 3.502 r_mcangle_it 2.391 r_mcangle_other 2.391
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 13.757 r_dihedral_angle_3_deg 13.352 r_long_range_B_refined 6.272 r_dihedral_angle_1_deg 6.2 r_long_range_B_other 6.107 r_scangle_other 5.469 r_scbond_it 3.504 r_scbond_other 3.502 r_mcangle_it 2.391 r_mcangle_other 2.391 r_mcbond_it 1.648 r_mcbond_other 1.621 r_angle_refined_deg 1.14 r_angle_other_deg 0.394 r_chiral_restr 0.065 r_gen_planes_refined 0.012 r_bond_refined_d 0.009 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 2478 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data scaling DIALS data reduction MOLREP phasing