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Crystal structure of a ketoreductase from Sphingobacterium siyangense SY1 with co-enzyme
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, SITTING DROP 298 25%PEG 550, 0.02M MgCl2, 0.1M Bis-Tris pH7.0
Crystal Properties Matthews coefficient Solvent content 2.73 55.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.434 α = 90 b = 84.434 β = 90 c = 280.321 γ = 120
Symmetry Space Group P 65 2 2
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 PILATUS3 2M 2023-10-16 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) 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 50 93.8 1 28.63 62.4 38601
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.12 0.845
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2 44.53 36683 1918 93.81 0.16801 0.16634 0.1796 0.20057 0.2137 RANDOM 41.636
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] 0.61 0.31 0.61 -1.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.917 r_long_range_B_refined 9.131 r_long_range_B_other 9.128 r_scangle_other 8.163 r_dihedral_angle_1_deg 6.387 r_dihedral_angle_2_deg 6.217 r_scbond_it 5.528 r_scbond_other 5.526 r_mcangle_it 4.777 r_mcangle_other 4.776
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.917 r_long_range_B_refined 9.131 r_long_range_B_other 9.128 r_scangle_other 8.163 r_dihedral_angle_1_deg 6.387 r_dihedral_angle_2_deg 6.217 r_scbond_it 5.528 r_scbond_other 5.526 r_mcangle_it 4.777 r_mcangle_other 4.776 r_mcbond_it 3.475 r_mcbond_other 3.475 r_angle_refined_deg 1.648 r_angle_other_deg 0.579 r_chiral_restr 0.088 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 3702 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction PHASER phasing