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Crystal structure of Escherichia coli Orotate Phosphoribosyltransferase in complex with Orotic acid 1.60 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 293 2.1 M (NH4)2SO4, 0.2 M NaCl, 0.3 M sodium citrate (pH 4.8)
Crystal Properties Matthews coefficient Solvent content 2.21 44.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.118 α = 90 b = 83.118 β = 90 c = 122.787 γ = 90
Symmetry Space Group P 41 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 2019-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979260 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 1.6 49.38 99.5 0.076 0.079 0.023 0.999 15.1 12.5 57672 29.94
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 1.6 1.64 93.6 2.264 2.372 0.695 0.442 11.2
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 wwPDB 6TAI 1.6 49.38 1.34 57358 2000 99.31 0.1959 0.1949 0.1996 0.2234 0.2245 45.88
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 17.0813 f_angle_d 0.8526 f_chiral_restr 0.0561 f_bond_d 0.009 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3192 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 34
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing