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Structural insights into the catalysis mechanism of M. smegmatis antimutator protein MutT2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RRK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 292 0.1 M MES monohydrate pH 6.0, 20%(v/v) Jeffamine M-600 pH 7.0
Crystal Properties Matthews coefficient Solvent content 1.98 36.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.84 α = 90 b = 59.87 β = 90 c = 31.5 γ = 90
Symmetry Space Group P 21 21 2
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 300 mm CCD 2014-12-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.8266 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.1 16.46 95.9 0.062 16 4.8 49097
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.1 1.16 93.4 0.77 3 4.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2rrk 1.1 16.46 46545 2511 95.46 0.14364 0.14204 0.17247 0.1833 RANDOM 19.154
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] 0.53 -0.27 -0.26
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 31.885 r_dihedral_angle_2_deg 30.756 r_long_range_B_refined 22.325 r_long_range_B_other 22.316 r_dihedral_angle_4_deg 13.171 r_rigid_bond_restr 13.084 r_mcangle_other 10.528 r_dihedral_angle_3_deg 10.519 r_mcangle_it 10.519 r_mcbond_it 8.037
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 31.885 r_dihedral_angle_2_deg 30.756 r_long_range_B_refined 22.325 r_long_range_B_other 22.316 r_dihedral_angle_4_deg 13.171 r_rigid_bond_restr 13.084 r_mcangle_other 10.528 r_dihedral_angle_3_deg 10.519 r_mcangle_it 10.519 r_mcbond_it 8.037 r_mcbond_other 7.984 r_dihedral_angle_1_deg 6.953 r_scangle_other 5.236 r_scbond_it 4.462 r_scbond_other 4.336 r_angle_other_deg 2.018 r_angle_refined_deg 1.643 r_chiral_restr 0.116 r_bond_refined_d 0.016 r_gen_planes_refined 0.012 r_gen_planes_other 0.01 r_bond_other_d 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_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 921 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing