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Distinct structural features of TFAM drive mitochondrial DNA packaging versus transcriptional activation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TQ6 PDB ENTRY 3TQ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 295 12% PEG8000, 22% glycerol, 0.04 M potassium phosphate monobasic, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.92 57.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.372 α = 79.86 b = 82.49 β = 85.48 c = 104.222 γ = 84.53
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M Rh coated mirrors 2012-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 1.0332 SSRL BL12-2
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 2.897 39 50 0.038 13.5 2 40810 35526 1 1
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 2.897
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 3TQ6 2.897 35.64 2 33743 1783 87.05 0.267 0.22345 0.22108 0.22 0.26744 0.2658 RANDOM 99.732
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] -2.88 -0.23 -0.16 2.59 5 0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.156 r_dihedral_angle_4_deg 19.822 r_dihedral_angle_3_deg 19.385 r_long_range_B_refined 15.691 r_mcangle_it 8.906 r_scbond_it 6.991 r_mcbond_it 5.71 r_dihedral_angle_1_deg 4.956 r_angle_refined_deg 1.391 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.156 r_dihedral_angle_4_deg 19.822 r_dihedral_angle_3_deg 19.385 r_long_range_B_refined 15.691 r_mcangle_it 8.906 r_scbond_it 6.991 r_mcbond_it 5.71 r_dihedral_angle_1_deg 4.956 r_angle_refined_deg 1.391 r_chiral_restr 0.094 r_bond_refined_d 0.009 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6408 Nucleic Acid Atoms 3577 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose MAR345dtb data collection PHASES phasing REFMAC refinement MOSFLM data reduction SCALA data scaling