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Crystal structure of Mycobacterium smegmatis MutT1 in complex with Ap5A, ATP and manganese
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 39.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.16 α = 90 b = 83.93 β = 93.63 c = 43.64 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 1.75 43.55 100 7.2 4.2 30580
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 1.84 100 1.8 4.2
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 5gg5 1.75 43.55 29013 1542 99.98 0.18073 0.17816 0.1871 0.22767 0.2321 RANDOM 31.893
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] -0.56 1.54 -2.42 2.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.2 r_dihedral_angle_4_deg 17.937 r_dihedral_angle_3_deg 14.842 r_long_range_B_refined 7.183 r_long_range_B_other 7.048 r_dihedral_angle_1_deg 6.997 r_scangle_other 5.099 r_mcangle_it 3.659 r_mcangle_other 3.658 r_scbond_it 3.395
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.2 r_dihedral_angle_4_deg 17.937 r_dihedral_angle_3_deg 14.842 r_long_range_B_refined 7.183 r_long_range_B_other 7.048 r_dihedral_angle_1_deg 6.997 r_scangle_other 5.099 r_mcangle_it 3.659 r_mcangle_other 3.658 r_scbond_it 3.395 r_scbond_other 3.385 r_mcbond_other 2.545 r_mcbond_it 2.544 r_angle_refined_deg 1.874 r_angle_other_deg 0.852 r_chiral_restr 0.101 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 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 2303 Nucleic Acid Atoms Solvent Atoms 293 Heterogen Atoms 79
Software Software Software Name Purpose REFMAC refinement iMOSFLM data processing SCALA data scaling PHASER phasing iMOSFLM data reduction