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S. cerevisiae orotate phosphoribosyltransferase complexed with orotic acid and PRPP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PRZ PDB ENTRY 2PRZ (S. cerevisiae OPRTase complexed with OMP)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 288.15 38% PEG 4000, 0.14M ammonium acetate, 0.1M sodium acetate, 2.0mM magnesium chloride, 5.0mM PRPP, 5.0mM orotic acid, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 288.15K
Crystal Properties Matthews coefficient Solvent content 2.04 39.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.788 α = 90.59 b = 50.051 β = 105.88 c = 50.078 γ = 92.99
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 ADSC QUANTUM 315 2006-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.98 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.75 50 92.9 0.049 0.043 17.8 3.6 39461 36660 0.2 21.245
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.81 63.7 0.251 0.211 3.2 2.5 2533
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2PRZ (S. cerevisiae OPRTase complexed with OMP) 1.75 49.94 39534 36660 1844 92.73 0.195 0.195 0.194 0.193 0.217 0.2182 RANDOM 23.628
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] 0.24 0.09 1.14 0.32 0.63 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.196 r_dihedral_angle_3_deg 14.733 r_dihedral_angle_4_deg 10.863 r_dihedral_angle_1_deg 4.831 r_scangle_it 1.536 r_angle_refined_deg 1.11 r_scbond_it 0.982 r_mcangle_it 0.853 r_mcbond_it 0.484 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.196 r_dihedral_angle_3_deg 14.733 r_dihedral_angle_4_deg 10.863 r_dihedral_angle_1_deg 4.831 r_scangle_it 1.536 r_angle_refined_deg 1.11 r_scbond_it 0.982 r_mcangle_it 0.853 r_mcbond_it 0.484 r_nbtor_refined 0.298 r_nbd_refined 0.18 r_symmetry_vdw_refined 0.139 r_symmetry_hbond_refined 0.111 r_xyhbond_nbd_refined 0.091 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3446 Nucleic Acid Atoms Solvent Atoms 322 Heterogen Atoms 68
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing