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Crystal structure of the orotidine-5'-monophosphate decarboxylase domain of human UMP synthase bound to 5-iodo-UMP
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 50.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.58 α = 90 b = 61.998 β = 113.27 c = 70.565 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 2006-08-26 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 1.95 40 92.1 0.101 10.3 3.1 37157
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) 1 1.95 2 65.4 0.382 2.6 2.6 2610
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 1.95 40 35268 1868 91.93 0.22305 0.22061 0.26819 0.2233 RANDOM 24.961
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] 1.47 3.6 -2.27 3.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.054 r_dihedral_angle_4_deg 16.924 r_dihedral_angle_3_deg 16.206 r_dihedral_angle_1_deg 6.04 r_scangle_it 2.039 r_angle_refined_deg 1.251 r_scbond_it 1.237 r_mcangle_it 0.902 r_angle_other_deg 0.897 r_mcbond_it 0.508
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.054 r_dihedral_angle_4_deg 16.924 r_dihedral_angle_3_deg 16.206 r_dihedral_angle_1_deg 6.04 r_scangle_it 2.039 r_angle_refined_deg 1.251 r_scbond_it 1.237 r_mcangle_it 0.902 r_angle_other_deg 0.897 r_mcbond_it 0.508 r_symmetry_vdw_other 0.251 r_nbd_refined 0.205 r_symmetry_hbond_refined 0.197 r_nbd_other 0.193 r_nbtor_refined 0.173 r_symmetry_vdw_refined 0.17 r_xyhbond_nbd_refined 0.167 r_mcbond_other 0.095 r_nbtor_other 0.084 r_chiral_restr 0.065 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 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 3908 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement