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Crystal structure of Orotate phosphoribosyltransferase from Streptococcus pyogenes
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 289 Tris-Cl, Ammonium sulfate, Lithium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.8 55.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.131 α = 90 b = 118.131 β = 90 c = 72.185 γ = 90
Symmetry Space Group P 42 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 CCD CUSTOM-MADE 2005-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97922 APS 19-BM
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 1.95 50 98.9 0.157 32.8 31 37927 37510 -5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.02 89.7 0.667 2.62 14.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 SAD THROUGHOUT 1.95 50 37278 37278 1860 98.67 0.19131 0.19131 0.18932 0.1915 0.22942 0.1871 RANDOM 7.965
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] 0.06 0.06 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.691 r_dihedral_angle_4_deg 25.516 r_dihedral_angle_3_deg 15.562 r_dihedral_angle_1_deg 5.93 r_scangle_it 4.071 r_scbond_it 2.621 r_angle_refined_deg 1.649 r_mcangle_it 1.379 r_mcbond_it 0.896 r_symmetry_vdw_refined 0.336
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.691 r_dihedral_angle_4_deg 25.516 r_dihedral_angle_3_deg 15.562 r_dihedral_angle_1_deg 5.93 r_scangle_it 4.071 r_scbond_it 2.621 r_angle_refined_deg 1.649 r_mcangle_it 1.379 r_mcbond_it 0.896 r_symmetry_vdw_refined 0.336 r_nbtor_refined 0.311 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.149 r_symmetry_hbond_refined 0.14 r_chiral_restr 0.118 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3135 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling HKL-3000 phasing SHELXD phasing SHELXE model building MLPHARE phasing DM phasing SOLVE phasing RESOLVE phasing O model building Coot model building CCP4 phasing