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Crystal structure of human phosphoribosyl pyrophosphate synthetase 1(PRPS1) chimera swapped with three residues from PRPS2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H06 2H06
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.1M Lithium sulfate, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.05 59.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.083 α = 90 b = 108.083 β = 90 c = 659.674 γ = 90
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 2019-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9873 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3.1 50.01 100 0.538 0.559 0.153 2.2 13.2 135705
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.21 0.645
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 2H06 3.1 50.01 1.34 133985 6684 98.7 0.199 0.196 0.198 0.25 0.2415 56.57
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 10.73 f_angle_d 1.711 f_chiral_restr 0.096 f_bond_d 0.012 f_plane_restr 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 42181 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 42
Software Software Software Name Purpose DENZO data reduction SCALA data scaling PHASER phasing PHENIX refinement HKL-3000 data reduction