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Crystal structure of APRT from Y. pseudotuberculosis with bound adenine (P63 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 30% PEG3350, 0.1M Tris-Hcl pH 8.5, 0.2M Sodium Acetate with 5mM adenine, 1mM Nickel Chloride and 5% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.62 53.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.074 α = 90 b = 121.074 β = 90 c = 50.035 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 PIXEL DECTRIS EIGER R 4M 2017-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.9677 ESRF BM30A
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 2 50 99.5 0.122 0.128 0.039 6.3 10.6 28327
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 2.03 96 0.681 0.734 0.264 0.75 6.7
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 50 26119 1269 96.27 0.1618 0.1602 0.1715 0.1919 0.1957 RANDOM 27.793
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] 0.34 0.17 0.34 -1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.691 r_dihedral_angle_4_deg 17.815 r_dihedral_angle_3_deg 14.842 r_dihedral_angle_1_deg 6.782 r_angle_refined_deg 2.413 r_angle_other_deg 1.173 r_chiral_restr 0.146 r_bond_refined_d 0.027 r_gen_planes_refined 0.013 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.691 r_dihedral_angle_4_deg 17.815 r_dihedral_angle_3_deg 14.842 r_dihedral_angle_1_deg 6.782 r_angle_refined_deg 2.413 r_angle_other_deg 1.173 r_chiral_restr 0.146 r_bond_refined_d 0.027 r_gen_planes_refined 0.013 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2759 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 30
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing