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Mutant R1722W of the dihydroorotase domain of human CAD protein bound to the substrate carbamoyl aspartate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4C6J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 100 mM Tris-HCl, 2.5 M sodium formate, 2 mM carbamoyl aspartate
Crystal Properties Matthews coefficient Solvent content 2.54 51.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.219 α = 90 b = 158.537 β = 90 c = 61.991 γ = 90
Symmetry Space Group C 2 2 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 PILATUS3 X 2M 2021-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87313 ESRF ID23-2
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 1.55 47.25 98.23 0.997 10.18 6.7 260707 15.67
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 1.55 1.605 0.784 2.39
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.55 47.25 1.36 58384 2840 98.23 0.139 0.1374 0.1396 0.172 0.1745 19.35
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 8.0307 f_angle_d 1.0883 f_chiral_restr 0.0605 f_plane_restr 0.0102 f_bond_d 0.0091
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2739 Nucleic Acid Atoms Solvent Atoms 370 Heterogen Atoms 39
Software Software Software Name Purpose EDNA data collection autoPROC data processing PHASER phasing REFMAC refinement PHENIX refinement