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Crystal structure of APRT from Y. pseudotuberculosis with bound adenine (C2 space group).
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 25% PEG3350, 0.1M Tris-Hcl pH 8.5, 0.2M Sodium Acetate with 5mM adenine and 5% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.83 56.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.714 α = 90 b = 77.873 β = 112.61 c = 54.074 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 IMAGE PLATE RIGAKU RAXIS IV 2017-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5417
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 50 95.9 0.034 0.039 0.017 42.5 5 15046
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 1.98 2.01 63.9 0.149 0.173 0.085 0.992 3.4
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 1.98 49.92 13968 704 93.5 0.1999 0.1984 0.2065 0.2303 0.2345 RANDOM 31.64
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] -2.08 -0.37 0.25 1.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.331 r_dihedral_angle_4_deg 20.84 r_dihedral_angle_3_deg 13.362 r_dihedral_angle_1_deg 5.884 r_angle_refined_deg 1.179 r_angle_other_deg 0.591 r_chiral_restr 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.331 r_dihedral_angle_4_deg 20.84 r_dihedral_angle_3_deg 13.362 r_dihedral_angle_1_deg 5.884 r_angle_refined_deg 1.179 r_angle_other_deg 0.591 r_chiral_restr 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1343 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing