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Crystal structure of Mycobacterium smegmatis MutT1 in complex with Ap5A, ATP and magnesium
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 2.02 39.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.21 α = 90 b = 83.87 β = 93.24 c = 43.65 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 2016-04-13 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 43.58 96.9 11 4 38776
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 81.5 2.4 3
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 1.6 43.58 36787 1936 96.79 0.17596 0.17423 0.183 0.20903 0.2184 RANDOM 29.976
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] -0.83 1.55 -1.71 2.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.568 r_dihedral_angle_4_deg 17.813 r_dihedral_angle_3_deg 13.738 r_long_range_B_refined 6.68 r_long_range_B_other 6.508 r_dihedral_angle_1_deg 6.218 r_scangle_other 4.462 r_mcangle_it 3.209 r_mcangle_other 3.208 r_scbond_it 2.936
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.568 r_dihedral_angle_4_deg 17.813 r_dihedral_angle_3_deg 13.738 r_long_range_B_refined 6.68 r_long_range_B_other 6.508 r_dihedral_angle_1_deg 6.218 r_scangle_other 4.462 r_mcangle_it 3.209 r_mcangle_other 3.208 r_scbond_it 2.936 r_scbond_other 2.926 r_mcbond_it 2.118 r_mcbond_other 2.108 r_angle_refined_deg 1.787 r_angle_other_deg 0.814 r_chiral_restr 0.096 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 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 342 Heterogen Atoms 79
Software Software Software Name Purpose REFMAC refinement iMOSFLM data processing SCALA data scaling PHASER phasing iMOSFLM data reduction