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W-formate dehydrogenase from Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris) - Dithionite reduced - anaerobic soaked with 58 bar CO2 for 1 min
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SDV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 22% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl
Crystal Properties Matthews coefficient Solvent content 2.24 45.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.993 α = 90 b = 124.845 β = 90 c = 150.48 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 EIGER X 4M 2022-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
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 1.83 64.442 88.57 0.9887 8.518 8.53 73531
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 1.83 1.988 0.4894
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 1.83 64.442 73468 3726 67.649 0.193 0.1902 0.199 0.2405 0.2465 23.749
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] 0.072 0.002 -0.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.498 r_dihedral_angle_4_deg 20.046 r_dihedral_angle_3_deg 13.832 r_dihedral_angle_1_deg 7.174 r_lrange_it 6.406 r_lrange_other 6.388 r_scangle_it 4.775 r_scangle_other 4.77 r_mcangle_other 3.879 r_mcangle_it 3.878
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.498 r_dihedral_angle_4_deg 20.046 r_dihedral_angle_3_deg 13.832 r_dihedral_angle_1_deg 7.174 r_lrange_it 6.406 r_lrange_other 6.388 r_scangle_it 4.775 r_scangle_other 4.77 r_mcangle_other 3.879 r_mcangle_it 3.878 r_scbond_it 3.189 r_scbond_other 3.18 r_mcbond_it 2.66 r_mcbond_other 2.659 r_angle_refined_deg 1.374 r_angle_other_deg 1.188 r_symmetry_nbd_refined 0.236 r_nbd_refined 0.195 r_symmetry_nbd_other 0.18 r_nbd_other 0.175 r_nbtor_refined 0.161 r_xyhbond_nbd_refined 0.139 r_symmetry_xyhbond_nbd_refined 0.112 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.066 r_symmetry_xyhbond_nbd_other 0.064 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9213 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms 227
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