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Crystal structure of 2-methylcitrate synthase (PrpC) from Pseudomonas aeruginosa in apo form.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TQG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 292 100 mM Bis-Tris pH 5.5, 15-25% PEG3350, 40 mM D-Xylose
Crystal Properties Matthews coefficient Solvent content 2.11 41.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.014 α = 90 b = 83.195 β = 101.93 c = 82.713 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER X 16M 2017-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 1.53 57.99 99.9 0.056 0.067 0.036 0.998 8.9 3.2 101668 19.11
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 1.53 1.57 99.8 0.936 1.128 0.622 0.562 1.2 3.1
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 THROUGHOUT 3TQG 1.53 57.99 1.33 100689 1995 98.87 0.1962 0.1959 0.1983 0.2126 0.1994 26.3302
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 17.407 f_angle_d 1.468 f_chiral_restr 0.096 f_bond_d 0.016 f_plane_restr 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5732 Nucleic Acid Atoms Solvent Atoms 291 Heterogen Atoms 37
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction DIALS data reduction PHASER phasing