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Inactive dihydroorotase-like domain of Chaetomium thermophilum CAD-like multifunctional protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4C6M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 291 A construct spanning the DHO-like and ATC domains of C. thermophilum CAD-like protein was used for crystallization at 5 mg/ml. Crystals appear after 2-3 weeks in conditions with 20% PEG 20,000 and 0.1 M citric acid pH 4.5. The crystals only contained the DHO-like domain of the construct that was cleaved off during crystallization.
Crystal Properties Matthews coefficient Solvent content 2.18 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.771 α = 90 b = 109.177 β = 90 c = 58.314 γ = 90
Symmetry Space Group P 21 21 2
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 S 6M 2015-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.93927 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 2.13 48 98.8 0.11 0.047 0.998 11.3 6.5 36234 33.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.13 2.25 97.9 0.984 0.411 0.702 2 6.6
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 4C6M 2.13 45.814 1.33 36184 1736 98.44 0.2004 0.1989 0.2001 0.232 0.2331
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 14.185 f_angle_d 0.606 f_chiral_restr 0.068 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5197 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHASER phasing