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Crystal structure of Mycobacterium smegmatis MutT1 in complex with phosphate and magnesium ions (excess magnesium, I)
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 8.5 293 0.2 M magnesium chloride hexahydrate, 0.1 M TRIS hydrochloride, 30% w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2 38.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.99 α = 90 b = 87.67 β = 99.93 c = 90.68 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 IMAGE PLATE MAR scanner 345 mm plate 2014-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54179
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 1.85 31.97 99.8 7.6 5.3 51169
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 1.85 1.95 99.3 1.9 5.2
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 1.85 31.97 48523 2594 99.71 0.22481 0.22252 0.2293 0.26724 0.2705 RANDOM 29.627
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] -1.22 1.72 -2.71 3.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.872 r_dihedral_angle_4_deg 16.562 r_dihedral_angle_3_deg 15.502 r_dihedral_angle_1_deg 6.633 r_long_range_B_refined 6.059 r_long_range_B_other 5.897 r_scangle_other 4.138 r_mcangle_other 3.258 r_mcangle_it 3.256 r_scbond_it 2.687
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.872 r_dihedral_angle_4_deg 16.562 r_dihedral_angle_3_deg 15.502 r_dihedral_angle_1_deg 6.633 r_long_range_B_refined 6.059 r_long_range_B_other 5.897 r_scangle_other 4.138 r_mcangle_other 3.258 r_mcangle_it 3.256 r_scbond_it 2.687 r_scbond_other 2.679 r_mcbond_it 2.172 r_mcbond_other 2.164 r_angle_refined_deg 1.727 r_angle_other_deg 0.828 r_chiral_restr 0.092 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 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 4558 Nucleic Acid Atoms Solvent Atoms 468 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing