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Crystal structure of short chain dehydrogenase reductase 9 (short chain dehydrogenase reductase 9C4) in complex with NADH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9B2F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 295 15% Jeffamine SD-2001, 0.1 M Na citrate pH 5.4
Crystal Properties Matthews coefficient Solvent content 3.04 59.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.116 α = 90 b = 74.205 β = 133.12 c = 102.771 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 2021-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.9791 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 50 99.3 0.033 0.999 10.5 4.5 52809
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 99.1 0.426 0.809 2 4.5
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 40 49599 2680 98.22 0.20334 0.20148 0.2142 0.23844 0.249 RANDOM 74.779
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] 6.28 4.2 -9.23 -1.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.886 r_dihedral_angle_4_deg 17.253 r_dihedral_angle_3_deg 16.814 r_dihedral_angle_1_deg 6.903 r_long_range_B_other 6.61 r_long_range_B_refined 6.609 r_scangle_other 5.151 r_mcangle_other 4.167 r_mcangle_it 4.166 r_scbond_it 3.239
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.886 r_dihedral_angle_4_deg 17.253 r_dihedral_angle_3_deg 16.814 r_dihedral_angle_1_deg 6.903 r_long_range_B_other 6.61 r_long_range_B_refined 6.609 r_scangle_other 5.151 r_mcangle_other 4.167 r_mcangle_it 4.166 r_scbond_it 3.239 r_scbond_other 3.239 r_mcbond_it 2.817 r_mcbond_other 2.814 r_angle_refined_deg 1.426 r_angle_other_deg 1.211 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 4599 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing