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Crystal structure of Mycobacterium smegmatis MutT1 in complex with 8-oxo-GTP, 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 2.03 39.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.01 α = 90 b = 83.95 β = 92.98 c = 44 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 1.6 43.94 99.9 10.8 4.5 40162
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 1.6 1.69 100 2.1 4.5
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 1.6 43.94 38109 2013 99.86 0.16732 0.16526 0.1759 0.20596 0.2137 RANDOM 28.233
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] -1.2 0.91 -0.35 1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.449 r_dihedral_angle_4_deg 16.763 r_dihedral_angle_3_deg 15.307 r_dihedral_angle_1_deg 6.595 r_long_range_B_refined 6.563 r_long_range_B_other 6.37 r_scangle_other 4.857 r_mcangle_it 3.214 r_mcangle_other 3.214 r_scbond_other 3.161
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.449 r_dihedral_angle_4_deg 16.763 r_dihedral_angle_3_deg 15.307 r_dihedral_angle_1_deg 6.595 r_long_range_B_refined 6.563 r_long_range_B_other 6.37 r_scangle_other 4.857 r_mcangle_it 3.214 r_mcangle_other 3.214 r_scbond_other 3.161 r_scbond_it 3.152 r_mcbond_it 2.222 r_mcbond_other 2.218 r_angle_refined_deg 1.977 r_angle_other_deg 0.871 r_chiral_restr 0.112 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.001 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 338 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing