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Crystal structure of the orotidine-5'-monophosphate decarboxylase domain of human UMP synthase bound to UMP
Crystallization Crystal Properties Matthews coefficient Solvent content 2.44 49.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.394 α = 90 b = 61.643 β = 112.71 c = 69.97 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate mirors 2006-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5419
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 2.03 42.3 98 0.095 18.6 6.2 34716
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.03 2.08 83.8 0.344 3.9 4.7 2961
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.03 42.26 32963 1733 98.49 0.15174 0.14947 0.1946 0.1902 RANDOM 20.797
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] -0.05 1.47 -1.18 2.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.246 r_dihedral_angle_4_deg 15.665 r_dihedral_angle_3_deg 13.817 r_dihedral_angle_1_deg 6.189 r_scangle_it 3.42 r_scbond_it 2.38 r_angle_refined_deg 1.388 r_mcangle_it 1.258 r_mcbond_it 1.175 r_angle_other_deg 0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.246 r_dihedral_angle_4_deg 15.665 r_dihedral_angle_3_deg 13.817 r_dihedral_angle_1_deg 6.189 r_scangle_it 3.42 r_scbond_it 2.38 r_angle_refined_deg 1.388 r_mcangle_it 1.258 r_mcbond_it 1.175 r_angle_other_deg 0.93 r_symmetry_vdw_other 0.292 r_nbd_refined 0.218 r_nbd_other 0.2 r_symmetry_vdw_refined 0.182 r_mcbond_other 0.182 r_symmetry_hbond_refined 0.18 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.145 r_nbtor_other 0.083 r_chiral_restr 0.08 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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 3943 Nucleic Acid Atoms Solvent Atoms 348 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling COMO phasing