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Covalent complex of the orotidine-5'-monophosphate decarboxylase domain of human UMP synthase with 6-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 2.44 49.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.448 α = 90 b = 61.912 β = 114.06 c = 70.28 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 2007-04-06 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 1.85 34.94 99.1 0.053 17.6 4.9 46040
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 1.85 1.9 79.9 0.271 2.9 2.7 1575
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 1.85 34.94 43717 2306 99.25 0.15795 0.15634 0.1645 0.18843 0.1953 RANDOM 25.916
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] 0.4 2.01 -1.06 2.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.42 r_dihedral_angle_4_deg 17.925 r_dihedral_angle_3_deg 14.957 r_dihedral_angle_1_deg 5.725 r_scangle_it 3.775 r_scbond_it 2.649 r_angle_refined_deg 1.474 r_mcangle_it 1.441 r_mcbond_it 1.375 r_angle_other_deg 0.943
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.42 r_dihedral_angle_4_deg 17.925 r_dihedral_angle_3_deg 14.957 r_dihedral_angle_1_deg 5.725 r_scangle_it 3.775 r_scbond_it 2.649 r_angle_refined_deg 1.474 r_mcangle_it 1.441 r_mcbond_it 1.375 r_angle_other_deg 0.943 r_symmetry_vdw_refined 0.271 r_symmetry_vdw_other 0.262 r_mcbond_other 0.233 r_nbd_refined 0.216 r_nbd_other 0.201 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.137 r_symmetry_hbond_refined 0.133 r_chiral_restr 0.091 r_nbtor_other 0.086 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 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 3929 Nucleic Acid Atoms Solvent Atoms 410 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling COMO phasing