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Crystal structure of the orotidine-5'-monophosphate decarboxylase domain (Asp312Asn mutant) of human UMP synthase bound to 6-hydroxymethyl-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 50.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.378 α = 90 b = 116.607 β = 90 c = 61.91 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 IMAGE PLATE MAR scanner 345 mm plate 2006-04-13 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 1.66 32.24 97.3 0.05 26 4.6 32717
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) 1.66 1.72 73.9 0.243 4.3 3.5 2466
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 1.67 32.24 31057 1640 98.62 0.14213 0.14123 0.1524 0.15927 0.169 RANDOM 20.58
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] 1.98 -0.9 -1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.345 r_dihedral_angle_4_deg 17.262 r_dihedral_angle_3_deg 13.073 r_dihedral_angle_1_deg 5.744 r_scangle_it 3.208 r_scbond_it 2.191 r_angle_refined_deg 1.421 r_mcbond_it 1.142 r_mcangle_it 1.113 r_angle_other_deg 0.919
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.345 r_dihedral_angle_4_deg 17.262 r_dihedral_angle_3_deg 13.073 r_dihedral_angle_1_deg 5.744 r_scangle_it 3.208 r_scbond_it 2.191 r_angle_refined_deg 1.421 r_mcbond_it 1.142 r_mcangle_it 1.113 r_angle_other_deg 0.919 r_symmetry_vdw_other 0.321 r_nbd_refined 0.226 r_nbd_other 0.206 r_mcbond_other 0.205 r_symmetry_vdw_refined 0.185 r_nbtor_refined 0.177 r_symmetry_hbond_refined 0.166 r_xyhbond_nbd_refined 0.126 r_nbtor_other 0.083 r_chiral_restr 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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 2125 Nucleic Acid Atoms Solvent Atoms 309 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement