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Structure of the PurE Phosphoribosylaminoimidazole Carboxylase Catalytic Subunit from Yersinia pestis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 1.6M ammonium sulphate, 4% maltose, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.58 52.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.04 α = 90 b = 114.04 β = 90 c = 231.74 γ = 90
Symmetry Space Group I 4 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD MARMOSAIC 300 mm CCD bimorph KB mirrors 2009-11-13 M SINGLE WAVELENGTH 2 1 x-ray 110 CCD MARMOSAIC 300 mm CCD bimorph KB mirrors 2009-11-12 M SINGLE WAVELENGTH 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.127 APS 21-ID-D 2 SYNCHROTRON APS BEAMLINE 21-ID-D 0.9763 APS 21-ID-D
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 1.4 50 99.1 0.104 14.2 11.8 147075 145751 1.7 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) 1,2 1.4 1.45 93.5 0.518 3 5.7 13631
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 SAD THROUGHOUT 1.41 34.3 3 147010 145702 7296 99.11 0.151 0.151 0.15 0.1689 0.167 0.181 RANDOM 12.154
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] -0.01 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.17 r_dihedral_angle_4_deg 20.262 r_dihedral_angle_3_deg 11.082 r_scangle_it 5.727 r_dihedral_angle_1_deg 5.361 r_scbond_it 3.669 r_mcangle_it 2.233 r_angle_refined_deg 1.631 r_mcbond_it 1.416 r_chiral_restr 0.113
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.17 r_dihedral_angle_4_deg 20.262 r_dihedral_angle_3_deg 11.082 r_scangle_it 5.727 r_dihedral_angle_1_deg 5.361 r_scbond_it 3.669 r_mcangle_it 2.233 r_angle_refined_deg 1.631 r_mcbond_it 1.416 r_chiral_restr 0.113 r_bond_refined_d 0.018 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4837 Nucleic Acid Atoms Solvent Atoms 861 Heterogen Atoms 70
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction BLU-MAX data collection HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing