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W-formate dehydrogenase from Desulfovibrio vulgaris - Soaking with Formate 22 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 2.26 45.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.684 α = 90 b = 123.874 β = 90 c = 149.181 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 16M 2021-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.7749 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.587 95.484 92.25 0.077 0.9982 11.336 4.68 1299786
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 1.587 1.7 0.5794
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6SDR 1.587 95.484 129786 6509 80.002 0.171 0.1695 0.1787 0.1923 0.2001 28.477
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] -0.035 -0.146 0.181
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.178 r_dihedral_angle_4_deg 17.968 r_dihedral_angle_3_deg 12.899 r_dihedral_angle_1_deg 7.09 r_lrange_it 6.794 r_lrange_other 6.781 r_scangle_it 5.745 r_scangle_other 5.745 r_scbond_it 4.099 r_scbond_other 4.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.178 r_dihedral_angle_4_deg 17.968 r_dihedral_angle_3_deg 12.899 r_dihedral_angle_1_deg 7.09 r_lrange_it 6.794 r_lrange_other 6.781 r_scangle_it 5.745 r_scangle_other 5.745 r_scbond_it 4.099 r_scbond_other 4.098 r_mcangle_other 3.971 r_mcangle_it 3.97 r_mcbond_it 3.087 r_mcbond_other 3.086 r_angle_refined_deg 1.387 r_angle_other_deg 1.297 r_nbd_other 0.215 r_nbd_refined 0.203 r_symmetry_nbd_other 0.18 r_nbtor_refined 0.164 r_symmetry_nbd_refined 0.162 r_symmetry_xyhbond_nbd_other 0.125 r_xyhbond_nbd_refined 0.116 r_symmetry_xyhbond_nbd_refined 0.103 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.076 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 9211 Nucleic Acid Atoms Solvent Atoms 458 Heterogen Atoms 192
Software Software Software Name Purpose REFMAC refinement autoPROC data processing STARANISO data scaling PHASER phasing autoPROC data reduction