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D312N mutant of human orotidyl-5'-monophosphate decarboxylase in complex with 6-cyano-UMP, covalent adduct
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 300 0.1 M Tris-HCl pH 8.0, 1.8 M (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 300.0K
Crystal Properties Matthews coefficient Solvent content 2.45 49.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.527 α = 90 b = 61.479 β = 113.13 c = 70.491 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 CCD MARMOSAIC 225 mm CCD 2008-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.00000 SLS X10SA
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 1.1 42.33 100 0.122 7 7.3 220824
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 1.1 1.13 99.9 0.815 2 6.2 11548
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 1.1 42.33 208905 10994 99.55 0.16264 0.16137 0.1704 0.18676 0.1924 RANDOM 12.155
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] 0.31 0.84 -0.46 0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.607 r_dihedral_angle_4_deg 13.953 r_dihedral_angle_3_deg 12.573 r_sphericity_free 6.714 r_dihedral_angle_1_deg 5.819 r_scangle_it 4.869 r_scbond_it 3.32 r_sphericity_bonded 2.992 r_mcangle_it 2.309 r_angle_other_deg 2.025
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.607 r_dihedral_angle_4_deg 13.953 r_dihedral_angle_3_deg 12.573 r_sphericity_free 6.714 r_dihedral_angle_1_deg 5.819 r_scangle_it 4.869 r_scbond_it 3.32 r_sphericity_bonded 2.992 r_mcangle_it 2.309 r_angle_other_deg 2.025 r_angle_refined_deg 1.67 r_mcbond_it 1.6 r_rigid_bond_restr 1.499 r_mcbond_other 0.689 r_chiral_restr 0.101 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 3932 Nucleic Acid Atoms Solvent Atoms 546 Heterogen Atoms 52
Software Software Software Name Purpose COMO phasing REFMAC refinement XDS data reduction SADABS data scaling