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2.8 Angstrom Crystal Structure of Type III Secretion Protein YscO from Vibrio parahaemolyticus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 295 Protein: 2.28 mG/mL, 0.5 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3; Screen: JCSG+ (C9), 0.1M Sodium/Potasium phosphate pH 6.2, 25% (v/v) 1,2 Propanediol, 10% (v/v) Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 4.13 70.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.114 α = 90 b = 149.114 β = 90 c = 63.422 γ = 90
Symmetry Space Group I 41 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 225 mm CCD Beryllium lenses 2013-08-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2.8 30 99.9 0.139 18.3 9.6 9084 9084 -3 55.3
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 2.8 2.85 100 0.603 4.2 10 436
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 2.8 29.24 8645 8645 434 99.69 0.19195 0.18946 0.1917 0.24308 0.2407 RANDOM 52.031
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] 0.46 0.46 -0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.165 r_dihedral_angle_4_deg 13.841 r_dihedral_angle_3_deg 11.605 r_long_range_B_refined 8.74 r_long_range_B_other 8.69 r_scangle_other 5.917 r_mcangle_it 4.262 r_mcangle_other 4.26 r_scbond_it 3.759 r_scbond_other 3.553
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.165 r_dihedral_angle_4_deg 13.841 r_dihedral_angle_3_deg 11.605 r_long_range_B_refined 8.74 r_long_range_B_other 8.69 r_scangle_other 5.917 r_mcangle_it 4.262 r_mcangle_other 4.26 r_scbond_it 3.759 r_scbond_other 3.553 r_mcbond_it 2.496 r_mcbond_other 2.468 r_dihedral_angle_1_deg 1.935 r_angle_refined_deg 1.649 r_angle_other_deg 0.718 r_chiral_restr 0.085 r_gen_planes_refined 0.019 r_gen_planes_other 0.017 r_bond_refined_d 0.01 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1347 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 10
Software Software Software Name Purpose Blu-Ice data collection SHELXS phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling