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Crystal structure of Xanthine-guanine phosphoribosyltransferase from Yersinia pestis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NUL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 0.2M Lithium sulphate, 25% PEG 3350, 0.1M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.7 54.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.557 α = 90 b = 66.557 β = 90 c = 165.379 γ = 90
Symmetry Space Group P 43 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 100 CCD ADSC QUANTUM 315 2013-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.074 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 66.56 99.9 0.067 0.054 0.069 0.018 0.987 10.6 14.4 39181 15.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.74 1.77 98.8 0.584 0.491 0.614 0.186 0.923 3.74 10.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 1NUL 1.74 66.56 37024 1931 99.43 0.16773 0.16626 0.1787 0.19654 0.2042 RANDOM 20.616
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] -0.2 -0.2 0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.039 r_dihedral_angle_4_deg 20.956 r_dihedral_angle_3_deg 13.421 r_dihedral_angle_1_deg 6.495 r_long_range_B_refined 4.16 r_long_range_B_other 4.09 r_scangle_other 2.817 r_mcangle_other 2.141 r_mcangle_it 2.139 r_angle_refined_deg 1.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.039 r_dihedral_angle_4_deg 20.956 r_dihedral_angle_3_deg 13.421 r_dihedral_angle_1_deg 6.495 r_long_range_B_refined 4.16 r_long_range_B_other 4.09 r_scangle_other 2.817 r_mcangle_other 2.141 r_mcangle_it 2.139 r_angle_refined_deg 1.84 r_scbond_it 1.749 r_scbond_other 1.749 r_mcbond_it 1.294 r_mcbond_other 1.267 r_angle_other_deg 0.795 r_chiral_restr 0.11 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2337 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction DENZO data reduction MOLREP phasing