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Ubiquitin-like domain of the mycobacterium tuberculosis type VII secretion system protein ECCD1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KV3 PDB entry 4KV3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 295 0.1M TRIS-HCL PH 8.5, 0.2M MAGNESIUM CHLORIDE,
30% PEG4000, vapor diffusion, sitting drop, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.28 46.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.72 α = 90 b = 46.72 β = 90 c = 279.02 γ = 120
Symmetry Space Group P 65 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 300 mm CCD 2012-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
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 1.88 46.5 100 0.106 20.64 13.4 15843 -3 30.083
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 1.88 1.93 100 0.996 3.07 13.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 4KV3 1.88 46.5 15842 794 99.97 0.1902 0.1879 0.2358 0.2285 RANDOM 29.184
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 -0.34 -0.34 1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.906 r_dihedral_angle_3_deg 13.031 r_dihedral_angle_4_deg 10.214 r_dihedral_angle_1_deg 5.603 r_angle_refined_deg 1.331 r_angle_other_deg 0.738 r_mcangle_it 0.698 r_mcbond_it 0.42 r_mcbond_other 0.42 r_chiral_restr 0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.906 r_dihedral_angle_3_deg 13.031 r_dihedral_angle_4_deg 10.214 r_dihedral_angle_1_deg 5.603 r_angle_refined_deg 1.331 r_angle_other_deg 0.738 r_mcangle_it 0.698 r_mcbond_it 0.42 r_mcbond_other 0.42 r_chiral_restr 0.072 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1332 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction SERGUI data collection XDS data reduction