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Pilotin from Vibrio vulnificus type 2 secretion system, EpsS.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FTF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293.15 0.1M tris Hcl pH 7.5
1.9M Amonium Sulfate
2.5% (v/v) PEG400
Crystal Properties Matthews coefficient Solvent content 2.7 54.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.83 α = 90 b = 83.21 β = 90 c = 90.79 γ = 90
Symmetry Space Group I 2 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 DECTRIS EIGER X 4M 2018-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) CC (Half) 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 1.75 45.39 99.3 0.13 0.999 14.14 16 14037 28.85
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.85 95.8 1.15 0.88 2.12
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 4FTF 1.75 45.39 12215 1822 99.38 0.18546 0.17904 0.1903 0.22787 0.2368 RANDOM 25.385
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] -1.34 -1.03 2.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.979 r_dihedral_angle_3_deg 13.749 r_dihedral_angle_4_deg 7.273 r_dihedral_angle_1_deg 6.227 r_long_range_B_refined 6.149 r_long_range_B_other 6.099 r_scangle_other 2.756 r_scbond_it 2.628 r_scbond_other 2.423 r_angle_refined_deg 1.397
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.979 r_dihedral_angle_3_deg 13.749 r_dihedral_angle_4_deg 7.273 r_dihedral_angle_1_deg 6.227 r_long_range_B_refined 6.149 r_long_range_B_other 6.099 r_scangle_other 2.756 r_scbond_it 2.628 r_scbond_other 2.423 r_angle_refined_deg 1.397 r_mcangle_it 1.35 r_mcangle_other 1.35 r_angle_other_deg 1.304 r_mcbond_it 1.149 r_mcbond_other 0.987 r_chiral_restr 0.079 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_gen_planes_other 0.003 r_bond_other_d 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 843 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling Arcimboldo phasing