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Structure of the soluble domain of EccB1 from the Mycobacterium smegmatis ESX-1 secretion system.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KK7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Protein storage buffer: 20 mM Tris, pH 8.0, 300 mM NaCl, 10% glycerol
Reservoir solution: 14% PEG 8000, 200 mM NaCl, 100 mM PO4-Citrate pH 4.2
Cryoprotectant: reservoir solution with 20% propylene glycol.
Crystal Properties Matthews coefficient Solvent content 2.61 52.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.41 α = 90 b = 74.41 β = 90 c = 280.6 γ = 120
Symmetry Space Group P 61 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 PIXEL PSI PILATUS 6M 2014-04-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9789 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 3.07 64.44 92.9 0.103 0.11 13.67 8.3 8748 -3 113.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.07 3.15 91.2 2.223 2.374 1.01 8.3
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 4KK7 3.07 64.44 7954 805 85.14 0.2464 0.2407 0.2544 0.2974 0.3066 RANDOM 91.15
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] -3.8784 -3.8784 7.7568
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 2.93 t_other_torsion 2.71 t_angle_deg 1.06 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 2.93 t_other_torsion 2.71 t_angle_deg 1.06 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2650 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing Coot model building BUSTER-TNT refinement PDB_EXTRACT data extraction