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Crystal structure of uracil-DNA glycosylase from cod (Gadus morhua) in complex with the proteinaceous inhibitor UGI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 17% PEG 4000, 4% PEG 550 MME, 0.27M LITHIUM SULFATE, 0.01M SODIUM BROMIDE, 0.1M TRIS-HCL, PH 7.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277.0K
Crystal Properties Matthews coefficient Solvent content 2.69 54.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.21 α = 90 b = 86.92 β = 90.35 c = 175.37 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 120 CCD ADSC QUANTUM 210 2009-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.94 175 91.2 0.073 10.76 2.94 199006 29.86
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 2.04 86.6 0.413 3.29 3.16
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 1.93 29.48 199005 10083 89.8 0.2393 0.2369 0.2402 0.2834 0.2868 RANDOM 25.036
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] 13.15 -4.31 5.65 -18.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.884 r_dihedral_angle_4_deg 15.505 r_dihedral_angle_3_deg 14.69 r_dihedral_angle_1_deg 6.427 r_mcangle_it 2.997 r_mcbond_it 2.193 r_mcbond_other 2.192 r_angle_refined_deg 1.668 r_angle_other_deg 0.866 r_chiral_restr 0.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.884 r_dihedral_angle_4_deg 15.505 r_dihedral_angle_3_deg 14.69 r_dihedral_angle_1_deg 6.427 r_mcangle_it 2.997 r_mcbond_it 2.193 r_mcbond_other 2.192 r_angle_refined_deg 1.668 r_angle_other_deg 0.866 r_chiral_restr 0.103 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19472 Nucleic Acid Atoms Solvent Atoms 1483 Heterogen Atoms
Software Software Software Name Purpose MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling