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Crystal structure of a VirB8-like protein of type IV secretion system from Rickettsia typhi
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 RityA.18390.a.B2 PS01633 at 11.2 mg/mL against CSHT A2, 0.4 M potassium sodium tartrate, cryo-protected with Al's oil, crystal grew over 7 months, crystal tracking ID 250519a2, unique puck ID zuk7-16, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.42 64.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.68 α = 90 b = 117.68 β = 90 c = 83.82 γ = 90
Symmetry Space Group P 41 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 2013-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2
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 1.95 50 100 0.065 24.26 9.6 43393 -3 30.753
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 1.95 2 100 0.477 4.15
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.95 50 43389 2182 99.97 0.1667 0.1656 0.1892 0.1862 RANDOM 31.9189
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] -1.07 -1.07 2.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.052 r_dihedral_angle_4_deg 22.704 r_dihedral_angle_3_deg 12.745 r_dihedral_angle_1_deg 6.865 r_mcangle_it 3.16 r_mcbond_it 2.009 r_mcbond_other 2.006 r_angle_refined_deg 1.464 r_angle_other_deg 0.805 r_chiral_restr 0.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.052 r_dihedral_angle_4_deg 22.704 r_dihedral_angle_3_deg 12.745 r_dihedral_angle_1_deg 6.865 r_mcangle_it 3.16 r_mcbond_it 2.009 r_mcbond_other 2.006 r_angle_refined_deg 1.464 r_angle_other_deg 0.805 r_chiral_restr 0.099 r_bond_refined_d 0.013 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 2226 Nucleic Acid Atoms Solvent Atoms 318 Heterogen Atoms 10
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction