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Catalytic core domain of Adenosine triphosphate phosphoribosyltransferase from Campylobacter jejuni with bound PRPP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UB9 single chain of 5UB9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293.15 0.1 M sodium acetate pH 5.0, 0.01 M ZnCl2, 7-10% PEG 6000
formed crystals were soaked with 3 mM PRPP for 30-60 min
Crystal Properties Matthews coefficient Solvent content 2.37 47.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.003 α = 90 b = 79.69 β = 90 c = 91.119 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 80 CCD ADSC QUANTUM 210r 2014-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.959 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.1 50 99.9 0.096 0.999 27.3 14.6 28897
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 98.5 0.8 0.896 3.7 14.4
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 single chain of 5UB9 2.14 45.56 25799 1371 99.97 0.2131 0.20931 0.1814 0.28334 0.2595 RANDOM 33.047
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] -17.1 3.62 13.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.314 r_sphericity_free 33.13 r_dihedral_angle_4_deg 18.905 r_sphericity_bonded 17.781 r_dihedral_angle_3_deg 13.523 r_dihedral_angle_1_deg 5.752 r_long_range_B_other 5.449 r_long_range_B_refined 5.448 r_scangle_other 5.232 r_scbond_it 4.495
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.314 r_sphericity_free 33.13 r_dihedral_angle_4_deg 18.905 r_sphericity_bonded 17.781 r_dihedral_angle_3_deg 13.523 r_dihedral_angle_1_deg 5.752 r_long_range_B_other 5.449 r_long_range_B_refined 5.448 r_scangle_other 5.232 r_scbond_it 4.495 r_scbond_other 4.492 r_mcangle_it 4.332 r_mcangle_other 4.332 r_rigid_bond_restr 3.787 r_mcbond_it 3.784 r_mcbond_other 3.714 r_angle_refined_deg 1.504 r_angle_other_deg 0.983 r_chiral_restr 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.003 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3351 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing