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Crystal Structure of Human APRT wild type in complex with PRPP and Mg2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DCI
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 2.25 45.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.26 α = 77.02 b = 47.35 β = 69.53 c = 47.44 γ = 61.78
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 2M 2014-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.45 44.33 90.8 0.039 0.039 0.998 9.7 1.6 54531
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.47 86.9 0.262 0.262 0.788 2.1 1.7 2647
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 5DCI 1.45 44.33 51787 2743 90.76 0.1423 0.1405 0.149 0.1755 0.1759 RANDOM 17.406
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] 0.12 0.61 -0.38 0.01 -0.1 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.925 r_dihedral_angle_4_deg 19.563 r_sphericity_free 14.407 r_dihedral_angle_3_deg 12.567 r_dihedral_angle_1_deg 6.011 r_rigid_bond_restr 6.001 r_sphericity_bonded 4.696 r_mcangle_it 1.584 r_mcbond_it 1.476 r_mcbond_other 1.476
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.925 r_dihedral_angle_4_deg 19.563 r_sphericity_free 14.407 r_dihedral_angle_3_deg 12.567 r_dihedral_angle_1_deg 6.011 r_rigid_bond_restr 6.001 r_sphericity_bonded 4.696 r_mcangle_it 1.584 r_mcbond_it 1.476 r_mcbond_other 1.476 r_angle_refined_deg 1.232 r_angle_other_deg 0.565 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2736 Nucleic Acid Atoms Solvent Atoms 296 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction Coot model building MxCuBE data collection XDS data reduction