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W-formate dehydrogenase from Desulfovibrio vulgaris - Soaking with Formate 3 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 24% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl
Crystal Properties Matthews coefficient Solvent content 2.29 46.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.992 α = 90 b = 123.751 β = 90 c = 150.358 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 2022-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.8856 ESRF ID23-1
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 2.356 150.36 98.3 0.992 9 4.8 49978
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 2.356 2.43 0.409
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 2.356 95.733 49943 2409 97.97 0.214 0.2128 0.2192 0.2477 0.2448 44.55
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] 0.82 -1.879 1.058
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.39 r_dihedral_angle_4_deg 17.55 r_dihedral_angle_3_deg 14.874 r_dihedral_angle_1_deg 6.977 r_lrange_it 5.247 r_lrange_other 5.247 r_mcangle_it 3.611 r_mcangle_other 3.611 r_scangle_it 3.499 r_scangle_other 3.499
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.39 r_dihedral_angle_4_deg 17.55 r_dihedral_angle_3_deg 14.874 r_dihedral_angle_1_deg 6.977 r_lrange_it 5.247 r_lrange_other 5.247 r_mcangle_it 3.611 r_mcangle_other 3.611 r_scangle_it 3.499 r_scangle_other 3.499 r_mcbond_it 2.313 r_mcbond_other 2.313 r_scbond_it 2.19 r_scbond_other 2.19 r_angle_refined_deg 1.282 r_angle_other_deg 1.097 r_symmetry_xyhbond_nbd_refined 0.274 r_nbd_refined 0.184 r_symmetry_nbd_other 0.178 r_nbd_other 0.173 r_nbtor_refined 0.157 r_symmetry_nbd_refined 0.148 r_xyhbond_nbd_refined 0.147 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.05 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9197 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 170
Software Software Software Name Purpose REFMAC refinement autoPROC data processing PHASER phasing autoPROC data reduction STARANISO data scaling