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2.00 Angstrom resolution crystal structure of a catalytic subunit of an aspartate carbamoyltransferase (pyrB) from Yersinia pestis CO92
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EKX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 295 7.4 mg/mL protein in 10 mM Tris/HCl pH 8.3, 0.25 M NaCl, 5 mM BME; The JCSG+ condition #2 (0.1 M tri-sodium citrate, 20% (w/v) PEG 3000), VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.3 46.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.62 α = 90 b = 120.409 β = 90 c = 126.698 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 CCD MARMOSAIC 225 mm CCD beryllium lenses 2010-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2 30 99.8 0.075 20.28 7.3 70940 70940 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.03 100 0.539 3.39 6.7 3480
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 THROUGHOUT 1EKX 2 30 67286 67286 3574 99.69 0.18134 0.17943 0.2094 0.21694 0.243 RANDOM 45.809
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] -0.27 1.59 -1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.225 r_dihedral_angle_4_deg 19.627 r_dihedral_angle_3_deg 12.484 r_scangle_it 3.89 r_dihedral_angle_1_deg 3.791 r_scbond_it 2.585 r_mcangle_it 1.687 r_angle_refined_deg 1.674 r_mcbond_it 1.012 r_angle_other_deg 0.924
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.225 r_dihedral_angle_4_deg 19.627 r_dihedral_angle_3_deg 12.484 r_scangle_it 3.89 r_dihedral_angle_1_deg 3.791 r_scbond_it 2.585 r_mcangle_it 1.687 r_angle_refined_deg 1.674 r_mcbond_it 1.012 r_angle_other_deg 0.924 r_mcbond_other 0.321 r_chiral_restr 0.113 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6731 Nucleic Acid Atoms Solvent Atoms 452 Heterogen Atoms 13
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling