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Clostridium beijerinckii aldo-keto reductase Cbei_3974 with NADPH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5T79
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 90 mM MOPS pH 7.6, 271 mM NH4Cl2, 2.7% PEG 8K, 10 mM NADPH, 2 mM 4-pyridine methanol
Crystal Properties Matthews coefficient Solvent content 3.18 61.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.165 α = 90 b = 109.165 β = 90 c = 72.157 γ = 90
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 6M 2017-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.75 54.58 100 0.082 0.094 0.997 13.3 7.4 42762 19.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.8 100 0.809 0.963 0.725 1.7 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 5T79 1.75 54.58 40627 2105 99.9 0.16605 0.16471 0.173 0.19274 0.2006 RANDOM 29.821
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] -0.25 -0.25 0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.818 r_dihedral_angle_4_deg 13.548 r_dihedral_angle_3_deg 12.536 r_long_range_B_refined 6.353 r_long_range_B_other 6.224 r_dihedral_angle_1_deg 6.041 r_scangle_other 2.35 r_angle_refined_deg 1.983 r_mcangle_it 1.643 r_mcangle_other 1.643
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.818 r_dihedral_angle_4_deg 13.548 r_dihedral_angle_3_deg 12.536 r_long_range_B_refined 6.353 r_long_range_B_other 6.224 r_dihedral_angle_1_deg 6.041 r_scangle_other 2.35 r_angle_refined_deg 1.983 r_mcangle_it 1.643 r_mcangle_other 1.643 r_angle_other_deg 1.558 r_scbond_it 1.546 r_scbond_other 1.546 r_mcbond_it 0.986 r_mcbond_other 0.984 r_chiral_restr 0.096 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_bond_other_d 0.004 r_gen_planes_other 0.002 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 2467 Nucleic Acid Atoms Solvent Atoms 264 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XDS data reduction Aimless data scaling PHASER phasing