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Crystal structure of a short-chain dehydrogenase from Lactobacillus fermentum with NADPH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8YAV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.1M MES pH 6.0, 0.05M calcium chloride, 43% PEG 200
Crystal Properties Matthews coefficient Solvent content 2.45 49.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.827 α = 90 b = 88.818 β = 90 c = 157.371 γ = 90
Symmetry Space Group C 2 2 21
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 PILATUS 6M 2022-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17B1 0.987 SSRF BL17B1
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 1.54 30 92.6 0.15 0.154 0.034 0.998 2.6 19 71115
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.54 1.6 90.1 1.204 0.322 0.813 1.3 13.3
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 1.54 29.47 67536 3467 92.42 0.21883 0.2174 0.2323 0.24772 0.2629 RANDOM 17.654
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] -0.05 0.2 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.114 r_dihedral_angle_2_deg 8.76 r_dihedral_angle_1_deg 8.323 r_long_range_B_refined 6.145 r_long_range_B_other 5.905 r_scangle_other 4.458 r_scbond_it 3.037 r_scbond_other 3.003 r_mcangle_it 2.481 r_mcangle_other 2.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.114 r_dihedral_angle_2_deg 8.76 r_dihedral_angle_1_deg 8.323 r_long_range_B_refined 6.145 r_long_range_B_other 5.905 r_scangle_other 4.458 r_scbond_it 3.037 r_scbond_other 3.003 r_mcangle_it 2.481 r_mcangle_other 2.48 r_mcbond_it 1.805 r_mcbond_other 1.805 r_angle_refined_deg 1.007 r_angle_other_deg 0.343 r_chiral_restr 0.057 r_bond_refined_d 0.012 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 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 3774 Nucleic Acid Atoms Solvent Atoms 427 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing