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Transition state analysis of adenosine triphosphate phosphoribosyltransferase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NH7 PDB:1NH7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293.15 1.6 M magnesium sulphate and 0.1 M, 2-(N-morpholino)ethanesulfonic acid
Crystal Properties Matthews coefficient Solvent content 3.16 61.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.758 α = 90 b = 134.758 β = 90 c = 111.005 γ = 120
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 210r 2015-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9537 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.4 80.43 100 0.143 0.492 0.773 20 20 15289
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:1NH7 2.4 80.43 14540 747 99.96 0.21749 0.21571 0.2191 0.25051 0.2483 RANDOM 55.545
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] 1.64 0.82 1.64 -5.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.637 r_dihedral_angle_4_deg 21.034 r_dihedral_angle_3_deg 14.881 r_dihedral_angle_1_deg 6.929 r_long_range_B_refined 4.401 r_long_range_B_other 4.389 r_scangle_other 2.063 r_mcangle_it 1.98 r_mcangle_other 1.979 r_angle_refined_deg 1.519
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.637 r_dihedral_angle_4_deg 21.034 r_dihedral_angle_3_deg 14.881 r_dihedral_angle_1_deg 6.929 r_long_range_B_refined 4.401 r_long_range_B_other 4.389 r_scangle_other 2.063 r_mcangle_it 1.98 r_mcangle_other 1.979 r_angle_refined_deg 1.519 r_scbond_it 1.303 r_scbond_other 1.302 r_mcbond_it 1.141 r_mcbond_other 1.141 r_angle_other_deg 0.958 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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 1981 Nucleic Acid Atoms Solvent Atoms 28 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing