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Crystal structure of Mycobacterium smegmatis MutT1 in complex with 8-oxo-GDP, 8-oxo-GMP and pyrophosphate
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 38.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.73 α = 90 b = 84.3 β = 94.01 c = 43.58 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 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 0.95372 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 1.75 43.47 100 9.1 5.9 30343
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 1.75 1.84 100 1.6 5.8
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 1.75 43.47 28782 1533 99.97 0.18015 0.17764 0.1863 0.22895 0.2372 RANDOM 36.38
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] -1.69 1.62 -1.85 3.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.904 r_dihedral_angle_4_deg 17.875 r_dihedral_angle_3_deg 15.598 r_long_range_B_refined 7.508 r_long_range_B_other 7.462 r_dihedral_angle_1_deg 6.766 r_scangle_other 5.834 r_mcangle_it 4.056 r_mcangle_other 4.055 r_scbond_other 4.036
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.904 r_dihedral_angle_4_deg 17.875 r_dihedral_angle_3_deg 15.598 r_long_range_B_refined 7.508 r_long_range_B_other 7.462 r_dihedral_angle_1_deg 6.766 r_scangle_other 5.834 r_mcangle_it 4.056 r_mcangle_other 4.055 r_scbond_other 4.036 r_scbond_it 4.024 r_mcbond_it 3.057 r_mcbond_other 3.055 r_angle_refined_deg 2.008 r_angle_other_deg 0.882 r_chiral_restr 0.117 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 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 2305 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing