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Adenosine triphosphate phosphoribosyltransferase from Campylobacter jejuni in complex with the inhibitors AMP and histidine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YB5 PDB entry 4YB5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293.15 Tris, Magnesium Chloride, PEG4000, AMP, histidine
Crystal Properties Matthews coefficient Solvent content 2.37 48.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.871 α = 90 b = 124.906 β = 115.86 c = 92.809 γ = 90
Symmetry Space Group P 1 21 1
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 2014-04-02 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) 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 1.98 39.58 98.1 0.059 2 3.9 127994
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 1.98 2.01 96.9 0.422 3.1 3.9
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 PDB entry 4YB5 1.98 39.58 121691 6709 98.14 0.19621 0.19517 0.2036 0.21477 0.2209 RANDOM 23.844
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] 0.76 -0.55 1.12 -0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.104 r_dihedral_angle_4_deg 15.136 r_dihedral_angle_3_deg 13.64 r_dihedral_angle_1_deg 5.716 r_long_range_B_refined 4.707 r_long_range_B_other 4.707 r_scangle_other 3.165 r_mcangle_it 2.302 r_mcangle_other 2.302 r_scbond_it 1.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.104 r_dihedral_angle_4_deg 15.136 r_dihedral_angle_3_deg 13.64 r_dihedral_angle_1_deg 5.716 r_long_range_B_refined 4.707 r_long_range_B_other 4.707 r_scangle_other 3.165 r_mcangle_it 2.302 r_mcangle_other 2.302 r_scbond_it 1.97 r_scbond_other 1.969 r_mcbond_it 1.456 r_mcbond_other 1.456 r_angle_refined_deg 1.372 r_angle_other_deg 1.242 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.004 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 13259 Nucleic Acid Atoms Solvent Atoms 714 Heterogen Atoms 255
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing