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Crystal structure of Uracil-DNA glycosylase (TM0511) from Thermotoga maritima at 1.90 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 8.5 277 TRIS pH 8.5, 8% PEG-8000, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K. cryo condition: 25% PEG-200.
Crystal Properties Matthews coefficient Solvent content 2.65 53.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.049 α = 90 b = 61.049 β = 90 c = 127.5 γ = 90
Symmetry Space Group P 43 21 2
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 ADSC 2004-03-03 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.0000, 0.9796, 0.9794 ALS 8.2.1
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 1.9 50 99.97 0.068 25.15 7.87 19816 37.82
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 1.9 1.97 99.95 0.841 2.03 6.13 1938
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 MAD THROUGHOUT 1.9 44.09 18702 1013 99.96 0.17886 0.17743 0.1911 0.20573 0.2147 RANDOM 25.426
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] 1.31 1.31 -2.62
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 9.483 r_scbond_it 6.419 r_dihedral_angle_1_deg 5.693 r_mcangle_it 3.691 r_mcbond_it 2.039 r_angle_refined_deg 1.671 r_angle_other_deg 0.867 r_symmetry_vdw_other 0.353 r_nbd_other 0.239 r_nbd_refined 0.208
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 9.483 r_scbond_it 6.419 r_dihedral_angle_1_deg 5.693 r_mcangle_it 3.691 r_mcbond_it 2.039 r_angle_refined_deg 1.671 r_angle_other_deg 0.867 r_symmetry_vdw_other 0.353 r_nbd_other 0.239 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.146 r_symmetry_hbond_refined 0.095 r_chiral_restr 0.091 r_nbtor_other 0.084 r_symmetry_vdw_refined 0.044 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_gen_planes_other 0.007 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1479 Nucleic Acid Atoms Solvent Atoms 114 Heterogen Atoms 11
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHARP phasing autoSHARP phasing REFMAC refinement