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Crystal structure of Mycobacterium tuberculosis OGT in complex with DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BHB 4BHB, 1T39 experimental model PDB 1T39 4BHB, 1T39
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277.15 0.2M Ammonium acetate, 22% PEG 3350, 0.1M Hepes
Crystal Properties Matthews coefficient Solvent content 2.49 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.481 α = 90 b = 102.905 β = 90 c = 137.093 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 PIXEL PSI PILATUS 6M 2013-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.972 ESRF ID29
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 3 82.3 99.7 0.15 8.78 4.8 12278
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.16 0.889 1.7 5
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 4BHB, 1T39 3 82.3 12278 628 99.69 0.19721 0.19362 0.1994 0.26473 0.2583 RANDOM 60.49
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] -3.12 5.73 -2.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.239 r_dihedral_angle_4_deg 20.304 r_dihedral_angle_3_deg 15.994 r_long_range_B_refined 8.218 r_long_range_B_other 8.217 r_dihedral_angle_1_deg 6.784 r_scangle_other 5.665 r_mcangle_it 4.578 r_mcangle_other 4.578 r_scbond_it 3.458
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.239 r_dihedral_angle_4_deg 20.304 r_dihedral_angle_3_deg 15.994 r_long_range_B_refined 8.218 r_long_range_B_other 8.217 r_dihedral_angle_1_deg 6.784 r_scangle_other 5.665 r_mcangle_it 4.578 r_mcangle_other 4.578 r_scbond_it 3.458 r_scbond_other 3.458 r_mcbond_it 2.825 r_mcbond_other 2.825 r_angle_refined_deg 1.371 r_angle_other_deg 0.863 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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 3725 Nucleic Acid Atoms 532 Solvent Atoms 8 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing