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W-formate dehydrogenase C872A from Desulfovibrio vulgaris
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8CM4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 20% PEG 3350 (w/v), 0.1 M Tris-HCl pH 8.5 and 0.2 M CaCl2
Crystal Properties Matthews coefficient Solvent content 2.29 46.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.44 α = 90 b = 261.055 β = 90.576 c = 126.209 γ = 90
Symmetry Space Group P 1 21 1
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 2021-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9763 ESRF ID30B
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 2.15 48.831 96.8 0.998 6.7 2.3 248226
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 2.15 2.19 0.453
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 2.15 48.831 248196 12240 96.766 0.187 0.184 0.1894 0.2396 0.2407 34.843
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] -0.199 -1.52 0.418 -0.189
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.847 r_dihedral_angle_4_deg 18.391 r_dihedral_angle_3_deg 15.213 r_dihedral_angle_1_deg 7.818 r_lrange_it 6.56 r_lrange_other 6.557 r_scangle_other 4.914 r_scangle_it 4.911 r_mcangle_it 4.559 r_mcangle_other 4.559
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.847 r_dihedral_angle_4_deg 18.391 r_dihedral_angle_3_deg 15.213 r_dihedral_angle_1_deg 7.818 r_lrange_it 6.56 r_lrange_other 6.557 r_scangle_other 4.914 r_scangle_it 4.911 r_mcangle_it 4.559 r_mcangle_other 4.559 r_scbond_other 3.217 r_scbond_it 3.215 r_mcbond_it 3.102 r_mcbond_other 3.102 r_angle_refined_deg 1.67 r_angle_other_deg 1.255 r_nbd_refined 0.206 r_nbd_other 0.191 r_symmetry_nbd_other 0.186 r_symmetry_xyhbond_nbd_refined 0.182 r_nbtor_refined 0.167 r_xyhbond_nbd_refined 0.165 r_symmetry_nbd_refined 0.162 r_chiral_restr 0.087 r_symmetry_nbtor_other 0.078 r_symmetry_xyhbond_nbd_other 0.04 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 37154 Nucleic Acid Atoms Solvent Atoms 963 Heterogen Atoms 560
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing