☰ Navigation Tabs
Crystal structure of an APRT from Yersinia pseudotuberculosis in complex with AMP.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MB6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 2.4M sodium malonate pH 7.0 these crystals were moved condition containing 25% PEG3350, 0.1M Tris-Hcl pH 8.5, 0.2M Sodium Acetate and soaked with 5mM AMP
Crystal Properties Matthews coefficient Solvent content 2.97 58.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.875 α = 90 b = 78.554 β = 116.56 c = 53.885 γ = 90
Symmetry Space Group C 1 2 1
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 315 2013-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.072 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.9 48.2 99.3 0.061 0.054 12.8 5.9 17719 19.6
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 1.9 1.93 99.8 0.812 3.21 5.9
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 4MB6 1.9 48.2 15497 834 91.25 0.1881 0.1867 0.193 0.2121 0.2098 RANDOM 26.827
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] -1.21 0.26 -1.62 1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.09 r_dihedral_angle_4_deg 18.748 r_dihedral_angle_3_deg 14.922 r_dihedral_angle_1_deg 6.586 r_angle_refined_deg 2.306 r_mcangle_it 1.852 r_mcbond_it 1.073 r_mcbond_other 1.071 r_angle_other_deg 0.915 r_chiral_restr 0.137
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.09 r_dihedral_angle_4_deg 18.748 r_dihedral_angle_3_deg 14.922 r_dihedral_angle_1_deg 6.586 r_angle_refined_deg 2.306 r_mcangle_it 1.852 r_mcbond_it 1.073 r_mcbond_other 1.071 r_angle_other_deg 0.915 r_chiral_restr 0.137 r_bond_refined_d 0.023 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1355 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms 26
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction MOLREP model building