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Crystal Structure of Human APRT-Tyr105Phe variant in complex with Adenine, PRPP and Mg2+, 30 days post crystallization (with AMP and PPi products fully generated)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LN6
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 46.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.17 α = 76.93 b = 47.79 β = 61.5 c = 47.92 γ = 69.41
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 315r 2015-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.98 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 44.62 92.8 0.126 0.982 9.7 3.8 29551
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 93.2 0.586 0.823 3.9
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 5LN6 1.8 44.62 28037 1510 92.81 0.1528 0.1512 0.1649 0.1828 0.1949 RANDOM 18.294
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] -0.11 -0.21 0.42 0.3 -0.1 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.419 r_dihedral_angle_4_deg 16.784 r_dihedral_angle_3_deg 12.144 r_dihedral_angle_1_deg 5.673 r_angle_refined_deg 1.382 r_angle_other_deg 0.632 r_chiral_restr 0.075 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.419 r_dihedral_angle_4_deg 16.784 r_dihedral_angle_3_deg 12.144 r_dihedral_angle_1_deg 5.673 r_angle_refined_deg 1.382 r_angle_other_deg 0.632 r_chiral_restr 0.075 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2734 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 65
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction PHASER phasing