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Crystal structure of APRT from Y. pseudotuberculosis in complex with adenine.
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 8.5 298 30% PEG4000, 0.1M Tris-Hcl pH 8.5, 0.2M Sodium Acetate with 5mM adenine and 5% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.79 55.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.958 α = 90 b = 78.65 β = 115.2 c = 53.679 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 PIXEL DECTRIS EIGER X 9M 2017-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.9677 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.05 48.57 98.1 0.05 0.061 0.034 0.996 9.9 2.9 13665
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.11 94.8 0.49 0.62 0.375 0.731 2.4
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 2.05 48.57 13011 651 97.86 0.1876 0.1855 0.194 0.2283 0.2253 RANDOM 58.491
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] 1.76 -0.78 -1.79 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.701 r_dihedral_angle_4_deg 19.741 r_dihedral_angle_3_deg 15.823 r_dihedral_angle_1_deg 6.242 r_angle_refined_deg 1.589 r_angle_other_deg 0.708 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.701 r_dihedral_angle_4_deg 19.741 r_dihedral_angle_3_deg 15.823 r_dihedral_angle_1_deg 6.242 r_angle_refined_deg 1.589 r_angle_other_deg 0.708 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1343 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 11
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction MOLREP phasing