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Mycobacterium tuberculosis Rv1957 SecB-like chaperone in complex with a ChAD peptide from Rv1956 HigA1 antitoxin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FX3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 285 25-27 % PEG 1500, calcium acetate 80-240 mM, 10 % DMSO, 100 mM Tris pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.06 40.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.86 α = 90 b = 89.96 β = 90 c = 91.34 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 6M-F 2016-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.072522 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.835 64.09 99.9 0.093 0.999 13.7 6.5 63188
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 1.835 1.867 99.6 0.796 0.338 2.3 6.7
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 1FX3 1.84 64.09 59790 3397 99.94 0.2144 0.21156 0.2174 0.26488 0.2668 RANDOM 33.913
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.586 r_dihedral_angle_4_deg 16.412 r_dihedral_angle_3_deg 15.05 r_long_range_B_other 7.5 r_long_range_B_refined 7.498 r_dihedral_angle_1_deg 6.704 r_scangle_other 5.633 r_mcangle_it 4.574 r_mcangle_other 4.573 r_scbond_it 3.743
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.586 r_dihedral_angle_4_deg 16.412 r_dihedral_angle_3_deg 15.05 r_long_range_B_other 7.5 r_long_range_B_refined 7.498 r_dihedral_angle_1_deg 6.704 r_scangle_other 5.633 r_mcangle_it 4.574 r_mcangle_other 4.573 r_scbond_it 3.743 r_scbond_other 3.742 r_mcbond_other 3.41 r_mcbond_it 3.409 r_angle_refined_deg 1.941 r_angle_other_deg 0.906 r_chiral_restr 0.12 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.001 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 4585 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing