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Crystal structure of the orotidine-5'-monophosphate decarboxylase domain (Asp312Asn mutant) of human UMP synthase bound to 5-fluoro-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 2.4 48.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.815 α = 90 b = 115.512 β = 90 c = 61.37 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 CCD MAR CCD 165 mm 2006-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8 EMBL/DESY, HAMBURG X13
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 1.22 22.14 99.8 0.083 21.4 6.4 81404
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 1.22 1.24 0.594 2.5 4.6 3900
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 1.22 22.14 77246 4111 99.69 0.12264 0.12128 0.1237 0.14838 0.1531 RANDOM 9.11
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] 0.95 -0.44 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.141 r_dihedral_angle_4_deg 16.047 r_dihedral_angle_3_deg 13.118 r_sphericity_free 9.432 r_dihedral_angle_1_deg 6.229 r_scangle_it 4.666 r_scbond_it 3.472 r_sphericity_bonded 2.92 r_mcangle_it 2.09 r_mcbond_it 1.924
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.141 r_dihedral_angle_4_deg 16.047 r_dihedral_angle_3_deg 13.118 r_sphericity_free 9.432 r_dihedral_angle_1_deg 6.229 r_scangle_it 4.666 r_scbond_it 3.472 r_sphericity_bonded 2.92 r_mcangle_it 2.09 r_mcbond_it 1.924 r_angle_refined_deg 1.84 r_rigid_bond_restr 1.735 r_angle_other_deg 1.047 r_mcbond_other 0.672 r_symmetry_vdw_other 0.331 r_symmetry_hbond_refined 0.317 r_symmetry_vdw_refined 0.282 r_nbd_refined 0.254 r_nbd_other 0.215 r_xyhbond_nbd_refined 0.211 r_nbtor_refined 0.198 r_chiral_restr 0.125 r_nbtor_other 0.094 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1967 Nucleic Acid Atoms Solvent Atoms 382 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement