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The (p)ppGpp-bound crystal structure of HPRT (hypoxanthine phosphoribosyltransferase)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H83 PDB entry 3H83
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.6 293.15 0.2 M ammonium tartrate dibasic, pH 6.6, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 4.2 70.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.611 α = 90 b = 82.611 β = 90 c = 174.916 γ = 120
Symmetry Space Group P 31 2 1
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 MARMOSAIC 300 mm CCD 2015-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 100 99.6 0.164 0.06 16.41 8.1 40594
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.18 99 0.489 0.724 1.22 6.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 3H83 2.105 40.2 1.34 40414 1986 98.94 0.2037 0.2017 0.2028 0.2439 0.2454
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.272 f_angle_d 0.812 f_chiral_restr 0.048 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2824 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms 116
Software Software Software Name Purpose PHENIX refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing