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Crystal structure of Mycobacterium smegmatis MutT1 in complex with ATP, magnesium fluoride and phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GG5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 8.5 293 0.2M sodium acetate trihydrate, 0.1M Tris-HCl pH 8.5, 30%(w/v) PEG4000
Crystal Properties Matthews coefficient Solvent content 2.13 42.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.05 α = 90 b = 64.44 β = 102.59 c = 103.04 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 2015-11-20 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 54.26 99.7 12.2 4.2 64503
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 98.3 2.1 3.8
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 5gg5 1.75 54.26 61216 3270 99.71 0.16824 0.16622 0.1757 0.20503 0.2056 RANDOM 33.191
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] -0.49 -0.3 2.75 -1.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.223 r_dihedral_angle_4_deg 17.966 r_dihedral_angle_3_deg 13.869 r_long_range_B_refined 7.327 r_long_range_B_other 7.238 r_dihedral_angle_1_deg 6.289 r_scangle_other 5.31 r_mcangle_it 3.903 r_mcangle_other 3.902 r_scbond_it 3.526
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.223 r_dihedral_angle_4_deg 17.966 r_dihedral_angle_3_deg 13.869 r_long_range_B_refined 7.327 r_long_range_B_other 7.238 r_dihedral_angle_1_deg 6.289 r_scangle_other 5.31 r_mcangle_it 3.903 r_mcangle_other 3.902 r_scbond_it 3.526 r_scbond_other 3.526 r_mcbond_it 2.788 r_mcbond_other 2.786 r_angle_refined_deg 1.851 r_angle_other_deg 0.864 r_chiral_restr 0.108 r_bond_refined_d 0.017 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 4552 Nucleic Acid Atoms Solvent Atoms 445 Heterogen Atoms 130
Software Software Software Name Purpose REFMAC refinement iMOSFLM data processing SCALA data scaling PHASER phasing iMOSFLM data reduction