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Crystal structure of the Phosphorybosylpyrophosphate synthetase from E. Coli
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 COUNTER-DIFFUSION 7.5 293 0.1 M TRIS-buffer pH 8.5, 0.3M NaCl, 2 mM MgCl2, 04% NaN3, 15% Ammonium Sulphate, COUNTER DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.89 57.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.599 α = 90 b = 104.599 β = 90 c = 125.78 γ = 120
Symmetry Space Group P 63 2 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 PSI PILATUS 6M 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 Sym 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 2.71 30 95.67 0.09 7.96 12.22 10949
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.71 29.36 10425 521 94.43 0.25237 0.24974 0.2526 0.30433 0.2969 RANDOM 52.14
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] 0.54 0.54 0.54 -1.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.447 r_dihedral_angle_3_deg 18.372 r_dihedral_angle_4_deg 13.366 r_dihedral_angle_1_deg 7.264 r_angle_refined_deg 1.519 r_angle_other_deg 0.834 r_chiral_restr 0.081 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.447 r_dihedral_angle_3_deg 18.372 r_dihedral_angle_4_deg 13.366 r_dihedral_angle_1_deg 7.264 r_angle_refined_deg 1.519 r_angle_other_deg 0.834 r_chiral_restr 0.081 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2339 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 1
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling