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Ketoreductase from module 1 of the 6-deoxyerythronolide B synthase (KR1) in complex with antibody fragment (Fab) 1D10
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FR0 PDB entry 2FR0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 285.15 1.9 M ammonium sulfate, 0.1 M Tris, pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.24 62.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 186.03 α = 90 b = 114.81 β = 96.53 c = 186.14 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 16M 2019-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 1.19499 SSRL BL14-1
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 2.75 92.6 97.6 0.071 0.074 0.02 1 23.4 14 95801
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 2.75 2.94 99.9 0.994 1.032 0.277 0.913 13.8
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 PDB entry 2FR0 2.75 39.59 95801 5043 99.58 0.2305 0.2283 0.2291 0.2709 0.2668 RANDOM 97.859
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] 2.07 0.9 -1.28 -0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.539 r_dihedral_angle_3_deg 21.212 r_dihedral_angle_4_deg 19.495 r_dihedral_angle_1_deg 8.412 r_angle_refined_deg 1.546 r_angle_other_deg 1.197 r_chiral_restr 0.063 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.539 r_dihedral_angle_3_deg 21.212 r_dihedral_angle_4_deg 19.495 r_dihedral_angle_1_deg 8.412 r_angle_refined_deg 1.546 r_angle_other_deg 1.197 r_chiral_restr 0.063 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19245 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing