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Crystal structure of the orotidine-5'-monophosphate decarboxylase domain (Asp312Asn mutant) of human UMP synthase bound to OMP
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 49.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.493 α = 90 b = 61.596 β = 113.58 c = 70.305 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 1.85 26 97.2 0.062 20 3.8 45421
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 1.92 85.5 0.286 3.4 2.9 3963
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 26 43118 2268 97.32 0.17391 0.17185 0.1811 0.21278 0.2216 RANDOM 24.202
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] 1.18 2.07 -1.16 1.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.105 r_dihedral_angle_4_deg 14.775 r_dihedral_angle_3_deg 14.137 r_dihedral_angle_1_deg 5.995 r_scangle_it 3.606 r_scbond_it 2.449 r_angle_refined_deg 1.498 r_mcangle_it 1.275 r_mcbond_it 1.182 r_angle_other_deg 0.961
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.105 r_dihedral_angle_4_deg 14.775 r_dihedral_angle_3_deg 14.137 r_dihedral_angle_1_deg 5.995 r_scangle_it 3.606 r_scbond_it 2.449 r_angle_refined_deg 1.498 r_mcangle_it 1.275 r_mcbond_it 1.182 r_angle_other_deg 0.961 r_symmetry_vdw_other 0.311 r_symmetry_hbond_refined 0.234 r_mcbond_other 0.223 r_nbd_refined 0.214 r_nbd_other 0.204 r_nbtor_refined 0.174 r_symmetry_vdw_refined 0.168 r_xyhbond_nbd_refined 0.156 r_chiral_restr 0.088 r_nbtor_other 0.086 r_bond_refined_d 0.015 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 3917 Nucleic Acid Atoms Solvent Atoms 406 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement