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Crystal structure of a periplasmic domain of the EpsAB fusion protein of the Vibrio vulnificus type II secretion system
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 220 mM Calcium Chloride, 20% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.29 46.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.821 α = 90 b = 44.523 β = 110.59 c = 51.04 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 87 CCD RAYONIX MX-300 2012-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9793 CLSI 08ID-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 1.55 50 93 0.056 3.5 35030 36885 1.4 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.59 93.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 SAD THROUGHOUT 1.55 47.78 36885 35030 1851 93.19 0.17615 0.1747 0.1879 0.20223 0.2137 RANDOM 27.642
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] -0.03 -0.02 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.732 r_dihedral_angle_4_deg 20.375 r_dihedral_angle_3_deg 16.519 r_scangle_it 6.61 r_dihedral_angle_1_deg 6.512 r_scbond_it 4.02 r_mcangle_it 2.472 r_angle_refined_deg 2.307 r_mcbond_it 1.41 r_chiral_restr 0.182
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.732 r_dihedral_angle_4_deg 20.375 r_dihedral_angle_3_deg 16.519 r_scangle_it 6.61 r_dihedral_angle_1_deg 6.512 r_scbond_it 4.02 r_mcangle_it 2.472 r_angle_refined_deg 2.307 r_mcbond_it 1.41 r_chiral_restr 0.182 r_bond_refined_d 0.027 r_gen_planes_refined 0.013 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1818 Nucleic Acid Atoms Solvent Atoms 253 Heterogen Atoms
Software Software Software Name Purpose MsDC data collection PHENIX model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing