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Crystal Structure of Human APRT wild type in complex with IMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DE6
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 2.28 46.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.585 α = 76.43 b = 47.625 β = 69.24 c = 47.846 γ = 61.29
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 PILATUS 6M 2014-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.966 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.52 44.6 92.5 0.051 11.9 3.6 46425
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 1.52 1.57 89.9 0.67 1.7 3.6
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 5DE6 1.52 44.6 46425 2494 92.53 0.1709 0.1698 0.1824 0.1931 0.2045 RANDOM 26.428
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] 0.17 0.45 -0.27 -0.33 0.11 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.802 r_dihedral_angle_4_deg 19.153 r_dihedral_angle_3_deg 11.893 r_dihedral_angle_1_deg 5.955 r_mcangle_it 3.015 r_mcbond_it 2.391 r_mcbond_other 2.378 r_angle_refined_deg 1.301 r_angle_other_deg 0.683 r_chiral_restr 0.254
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.802 r_dihedral_angle_4_deg 19.153 r_dihedral_angle_3_deg 11.893 r_dihedral_angle_1_deg 5.955 r_mcangle_it 3.015 r_mcbond_it 2.391 r_mcbond_other 2.378 r_angle_refined_deg 1.301 r_angle_other_deg 0.683 r_chiral_restr 0.254 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2697 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction Coot model building XDS data reduction