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Crystal structure of Mycobacterium smegmatis MutT1 in complex with 8-oxo-dGDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FJY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 4.6 293 0.2 M sodium acetate, 0.1 M sodium acetate trihydrate, 30% w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.33 47.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.492 α = 90 b = 87.892 β = 90 c = 95.202 γ = 90
Symmetry Space Group P 21 21 21
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 2015-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.82656 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 64.59 100 10.2 7.9 145101
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.1 1.16 99.9 1.9 7
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 3FJY 1.1 64.58 137324 7244 99.66 0.16079 0.15953 0.1597 0.1847 0.1849 RANDOM 17.32
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] -0.19 0.01 0.19
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.6 r_dihedral_angle_2_deg 31.473 r_dihedral_angle_4_deg 16.603 r_dihedral_angle_3_deg 12.605 r_sphericity_bonded 10.268 r_rigid_bond_restr 6.879 r_dihedral_angle_1_deg 6.263 r_long_range_B_refined 4.658 r_long_range_B_other 4.059 r_scangle_other 3.461
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.6 r_dihedral_angle_2_deg 31.473 r_dihedral_angle_4_deg 16.603 r_dihedral_angle_3_deg 12.605 r_sphericity_bonded 10.268 r_rigid_bond_restr 6.879 r_dihedral_angle_1_deg 6.263 r_long_range_B_refined 4.658 r_long_range_B_other 4.059 r_scangle_other 3.461 r_scbond_it 3.221 r_scbond_other 3.206 r_mcangle_it 2.09 r_mcangle_other 2.089 r_angle_refined_deg 1.99 r_mcbond_it 1.759 r_mcbond_other 1.747 r_angle_other_deg 1.056 r_chiral_restr 0.132 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_gen_planes_other 0.004 r_bond_other_d 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2293 Nucleic Acid Atoms Solvent Atoms 486 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing