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Crystal structure of the orotidine-5'-monophosphate decarboxylase domain of human UMP synthase bound to sulfate, glycerol, and chloride
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 295 pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.47 50.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.224 α = 90 b = 116.912 β = 90 c = 61.965 γ = 90
Symmetry Space Group C 2 2 21
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 MAR CCD 165 mm M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 EMBL/DESY, HAMBURG X13
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 1.42 34.8 84.4 0.079 21 6.7 45102
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 1.42 1.47 26.3 0.263 0.492 1.7 2.4 1381
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 1.43 34.79 42806 2295 86.41 0.14603 0.14504 0.1531 0.16485 0.1717 RANDOM 10.86
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] 1.23 -0.6 -0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.879 r_dihedral_angle_4_deg 14.822 r_dihedral_angle_3_deg 12.673 r_dihedral_angle_1_deg 5.591 r_scangle_it 2.856 r_scbond_it 1.991 r_angle_refined_deg 1.238 r_mcangle_it 0.991 r_mcbond_it 0.934 r_angle_other_deg 0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.879 r_dihedral_angle_4_deg 14.822 r_dihedral_angle_3_deg 12.673 r_dihedral_angle_1_deg 5.591 r_scangle_it 2.856 r_scbond_it 1.991 r_angle_refined_deg 1.238 r_mcangle_it 0.991 r_mcbond_it 0.934 r_angle_other_deg 0.88 r_symmetry_vdw_other 0.255 r_nbd_refined 0.225 r_nbd_other 0.197 r_symmetry_vdw_refined 0.191 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.163 r_symmetry_hbond_refined 0.157 r_mcbond_other 0.156 r_nbtor_other 0.082 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1964 Nucleic Acid Atoms Solvent Atoms 357 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling COMO phasing