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The crystal structure of Pseudomonas putida PcaR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IA2 PDB entry 2IA2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 298 1.8 M ammonium phosphate monobasic, 0.1 M sodium acetate, pH 4.6, 1% ethylene glycol, 2.5% 1-butyl-2,3-dimethylimidazolium tetrafluoroborate, soak with selenourea
Crystal Properties Matthews coefficient Solvent content 2.81 56.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.903 α = 90 b = 148.903 β = 90 c = 55.711 γ = 120
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 2019-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID .925 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 1.74 50 99.8 0.107 0.039 34.3 7.7 87124 29.73
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 0.664 0.263 0.825
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 2IA2 1.74 48.74 1.34 71919 2002 99.59 0.1774 0.1762 0.1767 0.2189 0.2187 RANDOM 40.37
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 13.428 f_angle_d 1.4017 f_chiral_restr 0.0884 f_bond_d 0.0144 f_plane_restr 0.0122
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3951 Nucleic Acid Atoms Solvent Atoms 437 Heterogen Atoms 45
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing PHENIX model building Coot model building