☰ Navigation Tabs
W-formate dehydrogenase from Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris) - Soaking with Formamide
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 298 22% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl
Crystal Properties Matthews coefficient Solvent content 2.15 42.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.094 α = 90 b = 148.557 β = 90 c = 64.212 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 PILATUS 6M 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) 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 1.734 94.784 92.85 0.9966 8.54 4.48 86871
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 1.734 1.887 0.6057
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 1.734 94.784 86869 4436 70.898 0.193 0.1916 0.1988 0.228 0.2324 29.479
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] -0.146 0.022 0.124
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.691 r_dihedral_angle_4_deg 17.958 r_dihedral_angle_3_deg 13.255 r_dihedral_angle_1_deg 6.986 r_lrange_it 5.948 r_lrange_other 5.928 r_scangle_it 4.557 r_scangle_other 4.557 r_mcangle_it 3.655 r_mcangle_other 3.654
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.691 r_dihedral_angle_4_deg 17.958 r_dihedral_angle_3_deg 13.255 r_dihedral_angle_1_deg 6.986 r_lrange_it 5.948 r_lrange_other 5.928 r_scangle_it 4.557 r_scangle_other 4.557 r_mcangle_it 3.655 r_mcangle_other 3.654 r_scbond_it 3.018 r_scbond_other 3.017 r_mcbond_it 2.584 r_mcbond_other 2.584 r_angle_refined_deg 1.27 r_angle_other_deg 1.151 r_nbd_other 0.193 r_nbd_refined 0.185 r_symmetry_nbd_other 0.175 r_symmetry_nbd_refined 0.172 r_nbtor_refined 0.158 r_symmetry_xyhbond_nbd_other 0.146 r_xyhbond_nbd_refined 0.127 r_symmetry_xyhbond_nbd_refined 0.125 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.057 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9168 Nucleic Acid Atoms Solvent Atoms 363 Heterogen Atoms 244
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