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Crystal Structure of Human APRT wild type in complex with Adenine, PRPP and Mg2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HND
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 NaOAc, PEG4000, Glycerol, Tris
Crystal Properties Matthews coefficient Solvent content 2.22 44.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.71 α = 90.05 b = 49.79 β = 93.48 c = 71.49 γ = 101.91
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 2013-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9762 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.94 71.351 90.9 0.109 0.132 0.075 6.7 2.8 45067 45067
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 2.04 85.1 0.168 0.168 0.206 0.117 3.9 2.7 6152
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 5HND 1.94 71.35 42796 2271 90.95 0.1984 0.1964 0.2045 0.2369 0.2421 RANDOM 15.915
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] 1.78 0.06 -0.26 -0.68 -0.1 -1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.007 r_dihedral_angle_4_deg 19.106 r_dihedral_angle_3_deg 13.726 r_dihedral_angle_1_deg 6.387 r_mcangle_it 1.157 r_angle_refined_deg 0.873 r_mcbond_it 0.732 r_mcbond_other 0.731 r_angle_other_deg 0.535 r_chiral_restr 0.048
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.007 r_dihedral_angle_4_deg 19.106 r_dihedral_angle_3_deg 13.726 r_dihedral_angle_1_deg 6.387 r_mcangle_it 1.157 r_angle_refined_deg 0.873 r_mcbond_it 0.732 r_mcbond_other 0.731 r_angle_other_deg 0.535 r_chiral_restr 0.048 r_gen_planes_refined 0.006 r_bond_other_d 0.005 r_bond_refined_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5466 Nucleic Acid Atoms Solvent Atoms 311 Heterogen Atoms 132
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PHASER phasing PDB_EXTRACT data extraction Coot model building iMOSFLM data reduction