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Catalytic core domain of Adenosine triphosphate phosphoribosyltransferase from Campylobacter jejuni with bound ATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UB9 single chain of PDB 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 ATP for 30-60 min
Crystal Properties Matthews coefficient Solvent content 2.41 48.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.166 α = 90 b = 79.921 β = 90 c = 92.245 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 2013-11-26 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 50 99.8 0.082 0.998 13.6 7.9 33714
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 2.05 100 0.549 0.948 3.3 8.1
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 PDB 5UB9 2 39.948 31912 1703 99.65 0.20928 0.20663 0.2194 0.25695 0.2677 RANDOM 39.073
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] 3.12 -1.81 -1.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.031 r_dihedral_angle_4_deg 20.699 r_dihedral_angle_3_deg 14.084 r_long_range_B_refined 6.573 r_long_range_B_other 6.539 r_dihedral_angle_1_deg 6.369 r_scangle_other 4.765 r_mcangle_it 3.644 r_mcangle_other 3.644 r_scbond_it 3.051
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.031 r_dihedral_angle_4_deg 20.699 r_dihedral_angle_3_deg 14.084 r_long_range_B_refined 6.573 r_long_range_B_other 6.539 r_dihedral_angle_1_deg 6.369 r_scangle_other 4.765 r_mcangle_it 3.644 r_mcangle_other 3.644 r_scbond_it 3.051 r_scbond_other 3.05 r_mcbond_it 2.491 r_mcbond_other 2.488 r_angle_refined_deg 1.562 r_angle_other_deg 0.95 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 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 3310 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing