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Macrodomain of Mycobacterium tuberculosis DarG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DX6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 200 mM ammonium chloride and 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.27 45.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.84 α = 90 b = 75.45 β = 90 c = 116.12 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 DECTRIS PILATUS 2M 2015-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.97625 Diamond I04-1
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 2.17 59.22 99.2 0.084 15.2 13.2 32503
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.17 2.23 98.4 2.302 0.658 1.5 13.2
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 2DX6 2.17 59.22 30882 1564 99.21 0.21375 0.21183 0.2144 0.25135 0.2497 RANDOM 71.173
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] 1.65 -4.59 2.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.484 r_dihedral_angle_4_deg 17.843 r_dihedral_angle_3_deg 13.91 r_long_range_B_refined 6.99 r_long_range_B_other 6.99 r_dihedral_angle_1_deg 5.809 r_scangle_other 4.929 r_mcangle_it 4.035 r_mcangle_other 4.035 r_scbond_it 3.021
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.484 r_dihedral_angle_4_deg 17.843 r_dihedral_angle_3_deg 13.91 r_long_range_B_refined 6.99 r_long_range_B_other 6.99 r_dihedral_angle_1_deg 5.809 r_scangle_other 4.929 r_mcangle_it 4.035 r_mcangle_other 4.035 r_scbond_it 3.021 r_scbond_other 3.021 r_mcbond_it 2.624 r_mcbond_other 2.624 r_angle_refined_deg 1.498 r_angle_other_deg 1.336 r_chiral_restr 0.084 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.007 r_gen_planes_other 0.006 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 4668 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing