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Aldo-keto reductase KmAKR - Y28A/K29H/T63M/Q213A/Y296W/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 7.5 291 Sodium acetate trihydrate, TRIS hydrochloride, Polyethylene glycol 4000, glycerol
Crystal Properties Matthews coefficient Solvent content 2.27 45.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.276 α = 90 b = 114.829 β = 101.32 c = 83.074 γ = 90
Symmetry Space Group P 1 21 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 2.39 114.83 99.8 0.217 0.237 0.093 0.952 6.2 6.5 49684
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 2.39 2.47 99.9 0.662 0.726 0.293 0.843 6.1
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 2.39 81.46 47104 2549 99.77 0.22293 0.21963 0.2212 0.28343 0.2806 RANDOM 27.755
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] 3.82 0.13 -0.32 -3.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.348 r_dihedral_angle_2_deg 9.215 r_dihedral_angle_1_deg 7.633 r_long_range_B_refined 6.965 r_long_range_B_other 6.96 r_scangle_other 5.281 r_mcangle_it 4.027 r_mcangle_other 4.027 r_scbond_it 3.226 r_scbond_other 3.226
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.348 r_dihedral_angle_2_deg 9.215 r_dihedral_angle_1_deg 7.633 r_long_range_B_refined 6.965 r_long_range_B_other 6.96 r_scangle_other 5.281 r_mcangle_it 4.027 r_mcangle_other 4.027 r_scbond_it 3.226 r_scbond_other 3.226 r_mcbond_it 2.574 r_mcbond_other 2.574 r_angle_refined_deg 0.9 r_angle_other_deg 0.308 r_chiral_restr 0.047 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 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 9745 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction MOLREP phasing