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Crystal structure of Mycobacterium smegmatis MutT1
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 6.5 293 0.2 M ammonium sulfate, 0.1 M MES monohydrate, 30% w/v PEG monomethyl ether 5000, 0.01M TCEP hydrochloride
Crystal Properties Matthews coefficient Solvent content 2.18 43.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.45 α = 90 b = 87.66 β = 90 c = 101.28 γ = 90
Symmetry Space Group P 21 21 21
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 2012-11-25 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 1.64 43.85 99.4 11.4 3.6 41476
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 1.64 1.73 96.3 3.6 3.2
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 1.64 43.85 39333 2094 99.21 0.15867 0.15664 0.1697 0.1974 0.2017 RANDOM 17.092
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] -0.44 -0.56 0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.277 r_dihedral_angle_4_deg 14.83 r_dihedral_angle_3_deg 13.17 r_long_range_B_refined 7.054 r_long_range_B_other 6.773 r_dihedral_angle_1_deg 6.33 r_scangle_other 3.824 r_scbond_it 2.618 r_scbond_other 2.617 r_mcangle_other 2.483
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.277 r_dihedral_angle_4_deg 14.83 r_dihedral_angle_3_deg 13.17 r_long_range_B_refined 7.054 r_long_range_B_other 6.773 r_dihedral_angle_1_deg 6.33 r_scangle_other 3.824 r_scbond_it 2.618 r_scbond_other 2.617 r_mcangle_other 2.483 r_mcangle_it 2.482 r_angle_refined_deg 2.034 r_mcbond_it 1.58 r_mcbond_other 1.565 r_angle_other_deg 0.904 r_chiral_restr 0.118 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.005 r_gen_planes_other 0.002 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 2310 Nucleic Acid Atoms Solvent Atoms 279 Heterogen Atoms 172
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing