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Crystal structure of Escherichia coli Orotate Phosphoribosyltransferase with an empty active site at 1.55 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ORO wwPDB 1ORO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 20% (w/v) PEG 6000, 0.2 M MgCl2, 0.1 M sodium acetate (pH 5.0)
Crystal Properties Matthews coefficient Solvent content 2.05 40.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.464 α = 90 b = 131.752 β = 90 c = 39.52 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 6M Kirkpatrick-Baez (KB) focusing mirrors 2019-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 1.03076 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 1.55 65.569 98.9 0.044 0.047 0.018 0.999 20.8 6.8 57472 25.78
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 1.551 1.556 89.5 0.903 0.997 0.407 0.68 1.6 5.5
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 1ORO 1.551 65.48 1.35 57394 2807 98.8 0.1781 0.1768 0.1804 0.2036 0.2056 40.44
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 22.8418 f_angle_d 0.6888 f_chiral_restr 0.0442 f_plane_restr 0.0041 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3193 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 10
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing