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Crystal Structure of Histone H3 Lysine 79 (H3K79) Methyltransferase Rv2067c from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Determined using iodine SAD; experimental phasing
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 Buffer: 0.1 M imidazole/MES acid, pH 6.5: Precipitant: 20% w/v polyethylene glycol 500* monomethyl ether + 10% w/v polyethylene glycol 20,000: Additive: 0.03 M sodium nitrate + 0.03 M sodium phosphate dibasic + 0.03 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.49 64.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.15 α = 90 b = 109.15 β = 90 c = 216.61 γ = 90
Symmetry Space Group P 41 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 PIXEL DECTRIS PILATUS3 6M 2018-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.699996 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 2.4 48.81 100 0.089 0.09 0.999 24.37 25.383 51986 71.257
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.46 100 2.223 2.268 0.741 1.71 25.633
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 Determined using iodine SAD; experimental phasing 2.4 48.81 49385 2600 99.98 0.2025 0.2017 0.2065 0.2183 0.2219 RANDOM 66.041
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] 0.5 0.5 -1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.279 r_dihedral_angle_4_deg 16.414 r_dihedral_angle_3_deg 14.85 r_dihedral_angle_1_deg 7.05 r_mcangle_it 2.767 r_mcbond_it 1.77 r_mcbond_other 1.77 r_angle_refined_deg 1.337 r_angle_other_deg 1.19 r_chiral_restr 0.059
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.279 r_dihedral_angle_4_deg 16.414 r_dihedral_angle_3_deg 14.85 r_dihedral_angle_1_deg 7.05 r_mcangle_it 2.767 r_mcbond_it 1.77 r_mcbond_other 1.77 r_angle_refined_deg 1.337 r_angle_other_deg 1.19 r_chiral_restr 0.059 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6068 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PHASER phasing CRANK2 phasing PDB_EXTRACT data extraction XDS data reduction