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W-formate dehydrogenase from Desulfovibrio vulgaris - aerobic soaked with 48 bar CO2 for 1 min
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 22% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl
Crystal Properties Matthews coefficient Solvent content 2.22 44.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.81 α = 90 b = 124.401 β = 90 c = 150.307 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 R 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 2.301 95.835 89.19 0.9854 6.55 5.6 45048
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 2.301 2.44 0.465
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 2.301 95.835 45013 2267 82.201 0.196 0.1938 0.2023 0.2442 0.2502 33.536
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] 0.131 -0.007 -0.124
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.551 r_dihedral_angle_4_deg 18.145 r_dihedral_angle_3_deg 16.189 r_dihedral_angle_1_deg 7.349 r_lrange_it 5.377 r_lrange_other 5.377 r_scangle_it 3.571 r_scangle_other 3.571 r_mcangle_it 3.464 r_mcangle_other 3.464
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.551 r_dihedral_angle_4_deg 18.145 r_dihedral_angle_3_deg 16.189 r_dihedral_angle_1_deg 7.349 r_lrange_it 5.377 r_lrange_other 5.377 r_scangle_it 3.571 r_scangle_other 3.571 r_mcangle_it 3.464 r_mcangle_other 3.464 r_scbond_it 2.295 r_scbond_other 2.292 r_mcbond_it 2.239 r_mcbond_other 2.237 r_angle_refined_deg 1.36 r_angle_other_deg 1.145 r_symmetry_nbd_refined 0.264 r_nbd_other 0.215 r_nbd_refined 0.198 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.162 r_xyhbond_nbd_refined 0.148 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.057 r_symmetry_xyhbond_nbd_refined 0.051 r_symmetry_xyhbond_nbd_other 0.008 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 9199 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 242
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