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Aldo-keto reductase KmAKR
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 citrate tribasic dihydrate, TRIS hydrochloride, Polyethylene glycol 400
Crystal Properties Matthews coefficient Solvent content 2.19 43.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.85 α = 90 b = 48.321 β = 90.04 c = 146.101 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 2023-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.9792 SSRF BL10U2
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 1.91 56.15 99.9 0.142 0.155 0.061 0.985 7.7 6.3 95916
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 1.91 1.94 100 0.25 0.276 0.115 0.898 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 1.91 56.15 91128 4774 99.73 0.20745 0.20523 0.2093 0.2501 0.2534 RANDOM 17.75
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] -5.81 3.73 -2.26 8.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.734 r_dihedral_angle_2_deg 12.314 r_dihedral_angle_1_deg 7.577 r_long_range_B_refined 5.608 r_long_range_B_other 5.572 r_mcangle_it 2.889 r_mcangle_other 2.888 r_scangle_other 2.734 r_mcbond_it 1.887 r_mcbond_other 1.887
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.734 r_dihedral_angle_2_deg 12.314 r_dihedral_angle_1_deg 7.577 r_long_range_B_refined 5.608 r_long_range_B_other 5.572 r_mcangle_it 2.889 r_mcangle_other 2.888 r_scangle_other 2.734 r_mcbond_it 1.887 r_mcbond_other 1.887 r_scbond_it 1.744 r_scbond_other 1.744 r_angle_refined_deg 0.746 r_angle_other_deg 0.257 r_chiral_restr 0.042 r_gen_planes_refined 0.011 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 9904 Nucleic Acid Atoms Solvent Atoms 538 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction MOLREP phasing