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Crystal structure of Escherichia coli Orotate Phosphoribosyltransferase in complex with Orotic acid and Sulfate at 1.25 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6TAI wwPDB 6TAI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.8 293 2.1 M (NH4)2SO4, 0.2 M NaCl, 0.3 M sodium citrate (pH 4.8)
Crystal Properties Matthews coefficient Solvent content 2.03 39.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.658 α = 90 b = 69.469 β = 90 c = 104.383 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 PILATUS3 6M Kirkpatrick-Baez (KB) focusing mirrors 2019-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.25 47.72 95.9 0.048 0.054 0.025 0.999 13.2 4.3 452457 17.56
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.28 68.8 1.386 1.722 1.001 0.292 2.3
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 wwPDB 6TAI 1.25 47.72 1.33 101164 1982 92.84 0.1816 0.1811 0.1814 0.2059 0.2036 26.23
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 15.8871 f_angle_d 1.2132 f_chiral_restr 0.0818 f_bond_d 0.0118 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3264 Nucleic Acid Atoms Solvent Atoms 375 Heterogen Atoms 103
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing