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Crystal structure of Mycobacterium smegmatis MutT1 in complex with 8-oxo-dGTP, 8-oxo-dGMP and pyrophosphate (I)
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 8.5 293 0.2 M sodium acetate trihydrate, 0.1 M TRIS hydrochloride, 30% w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.05 39.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42 α = 90 b = 85.35 β = 94.06 c = 87.43 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 2014-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54179
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 1.7 29.9 98.5 7.9 4.5 66623
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 1.7 1.79 96.5 1.8 4.4
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 1.7 29.9 63220 3366 98.44 0.19844 0.19645 0.2045 0.23624 0.2407 RANDOM 27.585
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] -0.5 0.81 -1.06 1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.587 r_dihedral_angle_4_deg 17.652 r_dihedral_angle_3_deg 16.051 r_dihedral_angle_1_deg 6.519 r_long_range_B_refined 6.492 r_long_range_B_other 6.313 r_scangle_other 4.562 r_mcangle_it 3.021 r_mcangle_other 3.02 r_scbond_other 2.908
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.587 r_dihedral_angle_4_deg 17.652 r_dihedral_angle_3_deg 16.051 r_dihedral_angle_1_deg 6.519 r_long_range_B_refined 6.492 r_long_range_B_other 6.313 r_scangle_other 4.562 r_mcangle_it 3.021 r_mcangle_other 3.02 r_scbond_other 2.908 r_scbond_it 2.903 r_mcbond_it 2.096 r_mcbond_other 2.092 r_angle_refined_deg 1.978 r_angle_other_deg 0.845 r_chiral_restr 0.1 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4589 Nucleic Acid Atoms Solvent Atoms 642 Heterogen Atoms 132
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing