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2.6 A crystal structure of uracil phosphoribosyltransferase from Burkholderia pseudomallei
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 289 2M NaCl, 5% PEG 4000, 0.1M TRIS, pH 8.5, VAPOR DIFFUSION, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.98 58.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.222 α = 90 b = 80.637 β = 99.11 c = 141.833 γ = 90
Symmetry Space Group C 1 2 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 CCD MARMOSAIC 300 mm CCD ADJUSTABLE FOCUSING MIRRORS 2008-04-04 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.00 APS 23-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 2.5 50 99.7 0.155 4.1 3.7 39360
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) 2.5 2.59 100 0.764 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 2.6 49.33 33305 1758 99.62 0.22145 0.21882 0.2175 0.27053 0.2676 RANDOM 45.41
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] -0.04 0.02 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.853 r_dihedral_angle_3_deg 20.261 r_dihedral_angle_4_deg 19.764 r_dihedral_angle_1_deg 6.713 r_scangle_it 2.3 r_angle_refined_deg 1.432 r_scbond_it 1.363 r_mcangle_it 1.027 r_mcbond_it 0.581 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.853 r_dihedral_angle_3_deg 20.261 r_dihedral_angle_4_deg 19.764 r_dihedral_angle_1_deg 6.713 r_scangle_it 2.3 r_angle_refined_deg 1.432 r_scbond_it 1.363 r_mcangle_it 1.027 r_mcbond_it 0.581 r_nbtor_refined 0.309 r_nbd_refined 0.221 r_symmetry_hbond_refined 0.215 r_symmetry_vdw_refined 0.212 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.095 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6694 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction