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Crystal structure of the Phosphorybosylpyrophosphate synthetase II from Thermus thermophilus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DKR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIQUID DIFFUSION 293 0.8M SA
Crystal Properties Matthews coefficient Solvent content 3.52 65.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.97 α = 90 b = 115.97 β = 90 c = 207.99 γ = 90
Symmetry Space Group P 41 21 2
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 PILATUS3 S 6M 2016-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.8 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.2 77.4 99.97 0.091 4.1075 11.43 72677
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.32 99.96 2.01 6.55
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 1DKR 2.2 64.39 69040 3548 99.95 0.22875 0.22742 0.2315 0.25443 0.2566 RANDOM 47.097
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] 0.03 0.03 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.259 r_dihedral_angle_3_deg 17.682 r_dihedral_angle_4_deg 16.232 r_dihedral_angle_1_deg 6.836 r_long_range_B_refined 5.618 r_long_range_B_other 5.605 r_mcangle_it 3.157 r_mcangle_other 3.157 r_scangle_other 3.132 r_mcbond_it 1.842
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.259 r_dihedral_angle_3_deg 17.682 r_dihedral_angle_4_deg 16.232 r_dihedral_angle_1_deg 6.836 r_long_range_B_refined 5.618 r_long_range_B_other 5.605 r_mcangle_it 3.157 r_mcangle_other 3.157 r_scangle_other 3.132 r_mcbond_it 1.842 r_mcbond_other 1.841 r_scbond_it 1.8 r_scbond_other 1.796 r_angle_refined_deg 1.453 r_angle_other_deg 1.001 r_chiral_restr 0.088 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6993 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms 111
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling BALBES phasing