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Octameric structure of the phosphoribosylaminoimidazole carboxylase catalytic subunit from Francisella tularensis subsp. tularensis SCHU S4.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OPQ PDB entry 3OPQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295 0.2 M NH4 Dihydrogen PO4, 0.1 M Tris, 6% MPD, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.92 36.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.56 α = 90 b = 96.3 β = 90 c = 128.62 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 MAR CCD MIRROR 2010-08-13 M MOLECULAR REPLACEMENT
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.75145 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 1.75 30 99 0.08 12.54 7.4 110138 110138 -3 31.8
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) 1.75 1.78 98.8 0.46 3.38 7.7 5387
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 SAD THROUGHOUT PDB entry 3OPQ 1.75 77.09 104329 104329 5493 29.38 0.17016 0.16833 0.1758 0.2051 0.2111 RANDOM 20.705
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] -0.99 2.69 -1.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.63 r_dihedral_angle_4_deg 22.651 r_dihedral_angle_3_deg 11.603 r_dihedral_angle_1_deg 5.154 r_scangle_it 4.625 r_scbond_it 3.158 r_mcangle_it 1.726 r_angle_refined_deg 1.5 r_angle_other_deg 0.962 r_mcbond_it 0.954
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.63 r_dihedral_angle_4_deg 22.651 r_dihedral_angle_3_deg 11.603 r_dihedral_angle_1_deg 5.154 r_scangle_it 4.625 r_scbond_it 3.158 r_mcangle_it 1.726 r_angle_refined_deg 1.5 r_angle_other_deg 0.962 r_mcbond_it 0.954 r_mcbond_other 0.276 r_chiral_restr 0.09 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9454 Nucleic Acid Atoms Solvent Atoms 545 Heterogen Atoms 170
Software Software Software Name Purpose Blu-Ice data collection CCP4 model building MrBUMP phasing PHENIX model building REFMAC refinement XSCALE data scaling CCP4 phasing PHENIX phasing