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Crystal structure of the core domain of Yersinia pestis virulence factor YopR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 291 17% PEG-8000, 85 mM Phosphate-citrate, 0.17 M NaCl, and 15% glycerol, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.1 40.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.662 α = 90 b = 85.662 β = 90 c = 85.662 γ = 90
Symmetry Space Group P 41 3 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 BRANDEIS 2003-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X9B 1 NSLS X9B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.5 22.82 99.3 0.036 0.036 46.1 4.5 17699 17807 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) 1.5 1.54 97.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MIR THROUGHOUT 1.499 22.81 2 17807 12054 640 71.36 0.2691 0.20526 0.20357 0.2207 0.23833 0.2564 RANDOM 21.596
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.588 r_scangle_it 3.013 r_scbond_it 1.762 r_mcangle_it 1.285 r_angle_refined_deg 1.019 r_angle_other_deg 0.743 r_mcbond_it 0.667 r_symmetry_vdw_refined 0.277 r_nbd_refined 0.25 r_nbd_other 0.222
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.588 r_scangle_it 3.013 r_scbond_it 1.762 r_mcangle_it 1.285 r_angle_refined_deg 1.019 r_angle_other_deg 0.743 r_mcbond_it 0.667 r_symmetry_vdw_refined 0.277 r_nbd_refined 0.25 r_nbd_other 0.222 r_xyhbond_nbd_refined 0.216 r_symmetry_hbond_refined 0.18 r_symmetry_vdw_other 0.177 r_nbtor_other 0.084 r_chiral_restr 0.057 r_bond_refined_d 0.008 r_gen_planes_other 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 771 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling SOLVE phasing