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Human orotidyl-5'-monophosphate decarboxylase in complex with 6-mercapto-UMP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 300 0.1M Tris-HCl pH 8.0, 1.8M (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 300.0K
Crystal Properties Matthews coefficient Solvent content 2.44 49.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.644 α = 90 b = 62.165 β = 113.99 c = 69.935 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 2007-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 1.74 34.65 97.6 0.078 12.6 4.9 53875 26.463
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) 1.75 1.79 80 0.575 1.4 2.6 2192
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 1.74 34.65 51149 2714 96.19 0.18182 0.18047 0.1972 0.20737 0.2218 RANDOM 22.011
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] -5.35 14.96 -14.23 19.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.621 r_dihedral_angle_4_deg 17.245 r_dihedral_angle_3_deg 14.11 r_dihedral_angle_1_deg 6.398 r_angle_refined_deg 1.61 r_angle_other_deg 0.985 r_chiral_restr 0.092 r_mcbond_it 0.026 r_mcbond_other 0.021 r_bond_refined_d 0.017
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.621 r_dihedral_angle_4_deg 17.245 r_dihedral_angle_3_deg 14.11 r_dihedral_angle_1_deg 6.398 r_angle_refined_deg 1.61 r_angle_other_deg 0.985 r_chiral_restr 0.092 r_mcbond_it 0.026 r_mcbond_other 0.021 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3944 Nucleic Acid Atoms Solvent Atoms 262 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement