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Crystal structure of molecular chaperone DnaK from Mycobacterium tuberculosis H37Rv
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V7Y PDB ENTRY 2V7Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.2 M Ammonium Chloride, 0.1 M HEPES, 20% PEG 6000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.27 45.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.866 α = 90 b = 117.866 β = 90 c = 134.943 γ = 120
Symmetry Space Group P 64 2 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 CCD MARMOSAIC 225 mm CCD beryllium lenses 2014-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2.77 30 99.8 0.07 52.8 21.4 14714 14714 -3
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 2.77 2.82 99.6 0.64 22
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2V7Y 2.77 30 13970 13970 724 99.74 0.21096 0.20803 0.26881 0.2663 RANDOM 68.437
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] -0.34 -0.17 -0.34 1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.902 r_dihedral_angle_3_deg 14.3 r_dihedral_angle_4_deg 11.597 r_long_range_B_refined 9.123 r_scbond_it 5.121 r_mcangle_it 4.634 r_mcbond_it 3.013 r_dihedral_angle_1_deg 2.487 r_angle_refined_deg 2.092 r_chiral_restr 0.158
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.902 r_dihedral_angle_3_deg 14.3 r_dihedral_angle_4_deg 11.597 r_long_range_B_refined 9.123 r_scbond_it 5.121 r_mcangle_it 4.634 r_mcbond_it 3.013 r_dihedral_angle_1_deg 2.487 r_angle_refined_deg 2.092 r_chiral_restr 0.158 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2584 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 22
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling