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Human dihydroorotase mutant F1563T co-crystallized with carbamoyl aspartate at pH 7.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4C6I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 Protein at 2-3 mg/ml in 20 mM Tris pH 8, 0.15 M NaCl, 0.02 mM zinc sulfate, 0.2 mM TCEP with 4 mM carbamoyl asparate.
Mother liquor: 2.5-3 M potassium formate, 0.1 M HEPES pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.53 51.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.104 α = 90 b = 158.948 β = 90 c = 61.21 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 PILATUS 6M 2014-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.0 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.19822864429 48.4940488716 99.6 0.046 0.999 21.6 6.4 124981 13.2304425898
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.19822864429 1.24 97.8 0.67 0.87 2.6 6.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 4c6i 1.19822864429 48.4940488716 1.33784209461 124947 6232 99.641934352 0.122501989216 0.121748467499 0.1258 0.1366740553 0.1399 21.0978390917
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 25.2330255754 f_angle_d 1.23383192953 f_chiral_restr 0.191102887667 f_bond_d 0.0106876891868 f_plane_restr 0.00929227358199
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2780 Nucleic Acid Atoms Solvent Atoms 513 Heterogen Atoms 27
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing