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Crystal structure of the outer membrane complex of a type IV secretion system
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other EMD-5034
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 20-40% w/v MPD, 100mM Bis-Tris pH 6.5-7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 3.6 65.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 202.4 α = 90 b = 211.63 β = 90 c = 203.44 γ = 90
Symmetry Space Group P 21 21 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 ADSC QUANTUM 315r torroidal focussing mirrors 2009-02-12 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315r Adjustable focus mirrors 2009-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9755 ESRF ID14-4 2 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.979 SOLEIL PROXIMA 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 2.6 52.91 95.5 0.055 12.12 1.98 519405 496105 1 1 42
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 2.6 2.8 94.7 0.264 3.11 1.98 98005
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 EMDB entry 5034, Cryo-EM structure of trypsin digested core TraF/TraN/TraO complex 2.6 52.91 1 496104 12939 95.5 0.22885 0.22725 0.206 0.25935 0.2307 RANDOM 37.277
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] -2.54 5.12 -2.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.873 r_dihedral_angle_4_deg 20.24 r_dihedral_angle_3_deg 19.088 r_dihedral_angle_1_deg 8.146 r_scangle_it 4.962 r_scbond_it 3.123 r_angle_refined_deg 1.985 r_mcangle_it 1.678 r_mcbond_it 0.865 r_chiral_restr 0.138
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.873 r_dihedral_angle_4_deg 20.24 r_dihedral_angle_3_deg 19.088 r_dihedral_angle_1_deg 8.146 r_scangle_it 4.962 r_scbond_it 3.123 r_angle_refined_deg 1.985 r_mcangle_it 1.678 r_mcbond_it 0.865 r_chiral_restr 0.138 r_bond_refined_d 0.02 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 37512 Nucleic Acid Atoms Solvent Atoms 1290 Heterogen Atoms 40
Software Software Software Name Purpose ADSC data collection AMoRE phasing REFMAC refinement XDS data reduction XSCALE data scaling