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Structure of ATP-phosphoribosyltransferase from E. coli complexed with PR-ATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H3D PDB ENTRY 1H3D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 298 sodium tartrate, magnesium chloride, sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.85 56.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.1 α = 90 b = 132.1 β = 90 c = 113.379 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 4 2002-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 0.86 SRS PX9.6
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 2.9 50 99.3 0.058 16.9 4.2 8521 8521 2 2
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 2.9 3.02 99.9 0.581 2 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1H3D 2.9 50 8521 7834 687 99.24 0.21454 0.21454 0.20967 0.27243 RANDOM 44.098
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] 3.04 1.52 3.04 -4.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.807 r_scangle_it 3.842 r_scbond_it 2.255 r_angle_refined_deg 2.018 r_mcangle_it 1.424 r_mcbond_it 0.736 r_nbd_refined 0.264 r_symmetry_hbond_refined 0.257 r_symmetry_vdw_refined 0.242 r_xyhbond_nbd_refined 0.147
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.807 r_scangle_it 3.842 r_scbond_it 2.255 r_angle_refined_deg 2.018 r_mcangle_it 1.424 r_mcbond_it 0.736 r_nbd_refined 0.264 r_symmetry_hbond_refined 0.257 r_symmetry_vdw_refined 0.242 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.126 r_bond_refined_d 0.018 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2187 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing