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Crystal structure of the Phosphorybosylpyrophosphate synthetase II from Thermus thermophilus at R32 space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5T3O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 COUNTER-DIFFUSION 293 1,7M lithium sulphate, 0,1M HEPES pH 7.5, 0,04%NaN3, 5mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.7 54.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.29 α = 90 b = 106.29 β = 90 c = 333.29 γ = 120
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 EIGER X 16M 2019-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.9790 SPring-8 BL41XU
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 1.85 20 100 0.105 0.999 14.31 7.01 59412
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 1.85 1.89 0.546 0.905
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 5T3O 1.85 19.77 59101 3111 99.82 0.1879 0.1862 0.1954 0.2212 0.2282 RANDOM 23.235
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] -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.922 r_dihedral_angle_4_deg 17.301 r_dihedral_angle_3_deg 16.194 r_dihedral_angle_1_deg 7.197 r_angle_refined_deg 1.668 r_angle_other_deg 1.415 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.922 r_dihedral_angle_4_deg 17.301 r_dihedral_angle_3_deg 16.194 r_dihedral_angle_1_deg 7.197 r_angle_refined_deg 1.668 r_angle_other_deg 1.415 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4720 Nucleic Acid Atoms Solvent Atoms 252 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction SCALA data scaling PHASER phasing