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W-formate dehydrogenase Q447A from Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SDR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 24% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl
Crystal Properties Matthews coefficient Solvent content 2.26 45.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.946 α = 90 b = 127.011 β = 90 c = 149.158 γ = 90
Symmetry Space Group P 21 21 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 EIGER2 S 9M 2023-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8731 ESRF ID23-2
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 2.123 59.546 91.5 0.985 6.3 6.5 59308
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 2.123 2.26 0.638
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.123 59.546 59270 2920 84.044 0.215 0.2129 0.2211 0.2609 0.271 33.121
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] 0.205 -0.142 -0.063
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.946 r_dihedral_angle_4_deg 21.305 r_dihedral_angle_3_deg 14.565 r_dihedral_angle_1_deg 7.56 r_lrange_it 3.632 r_lrange_other 3.621 r_mcangle_it 2.224 r_mcangle_other 2.224 r_scangle_it 1.965 r_scangle_other 1.964
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.946 r_dihedral_angle_4_deg 21.305 r_dihedral_angle_3_deg 14.565 r_dihedral_angle_1_deg 7.56 r_lrange_it 3.632 r_lrange_other 3.621 r_mcangle_it 2.224 r_mcangle_other 2.224 r_scangle_it 1.965 r_scangle_other 1.964 r_angle_refined_deg 1.47 r_mcbond_it 1.33 r_mcbond_other 1.33 r_angle_other_deg 1.173 r_scbond_it 1.166 r_scbond_other 1.166 r_nbd_other 0.241 r_nbd_refined 0.194 r_symmetry_nbd_other 0.185 r_nbtor_refined 0.162 r_xyhbond_nbd_refined 0.159 r_symmetry_nbd_refined 0.15 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.069 r_symmetry_xyhbond_nbd_other 0.046 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9179 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms 183
Software Software Software Name Purpose REFMAC refinement autoPROC data processing STARANISO data scaling PHASER phasing XDS data reduction Aimless data scaling XSCALE data scaling pointless data scaling