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Crystal structure of butanol dehydrogenase A (YqdH) in complex with NADH from Fusobacterium nucleatum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6L1K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 279.15 ammonium phosphate, HEPES
Crystal Properties Matthews coefficient Solvent content 3.14 60.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.426 α = 90 b = 79.351 β = 90 c = 212.932 γ = 90
Symmetry Space Group I 2 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 X CdTe 2M 2021-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17B1 0.9796 SSRF BL17B1
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 2.719 35.53 98.64 0.929 11.88 12.4 14920
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 2.719 2.817 0.531
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 6L1K 2.72 35.53 13427 1493 98.54 0.20356 0.19738 0.2084 0.25799 0.2598 RANDOM 56.195
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] 0.16 -0.33 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.015 r_long_range_B_refined 11.674 r_long_range_B_other 11.633 r_dihedral_angle_2_deg 11.074 r_scangle_other 8.858 r_mcangle_it 7.448 r_mcangle_other 7.447 r_dihedral_angle_1_deg 6.324 r_scbond_it 5.974 r_scbond_other 5.935
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.015 r_long_range_B_refined 11.674 r_long_range_B_other 11.633 r_dihedral_angle_2_deg 11.074 r_scangle_other 8.858 r_mcangle_it 7.448 r_mcangle_other 7.447 r_dihedral_angle_1_deg 6.324 r_scbond_it 5.974 r_scbond_other 5.935 r_mcbond_it 4.994 r_mcbond_other 4.991 r_angle_refined_deg 1.464 r_angle_other_deg 0.491 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 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 3004 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 51
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling PHENIX phasing HKL-2000 data collection