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Xenopus SMUG1, an anti-mutator uracil-DNA Glycosylase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other NATIVE STRUCTURE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.88 56.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.969 α = 90 b = 86.518 β = 118.53 c = 78.456 γ = 90
Symmetry Space Group C 1 2 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 ADSC CCD 2002-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 2.65 50 99.4 0.092 6.3 4.1 20624
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 2.65 2.79 96 0.438 1.6 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 NATIVE STRUCTURE 2.65 69.01 19561 1063 99.4 0.157 0.154 0.166 0.218 0.2181 RANDOM 44.55
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] 1.72 2.3 -0.08 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 9.143 r_scangle_it 8.203 r_scbond_it 5.112 r_angle_refined_deg 4.073 r_angle_other_deg 3.405 r_mcangle_it 3.316 r_mcbond_it 1.836 r_nbd_refined 0.315 r_nbd_other 0.298 r_xyhbond_nbd_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 9.143 r_scangle_it 8.203 r_scbond_it 5.112 r_angle_refined_deg 4.073 r_angle_other_deg 3.405 r_mcangle_it 3.316 r_mcbond_it 1.836 r_nbd_refined 0.315 r_nbd_other 0.298 r_xyhbond_nbd_refined 0.296 r_symmetry_vdw_other 0.277 r_chiral_restr 0.212 r_symmetry_vdw_refined 0.162 r_nbtor_other 0.127 r_symmetry_hbond_refined 0.095 r_bond_refined_d 0.051 r_gen_planes_refined 0.018 r_gen_planes_other 0.012 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined 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 r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3869 Nucleic Acid Atoms 478 Solvent Atoms 110 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling