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The structure of Yersinia pestis V-antigen, an essential virulence factor and mediator of immunity against plague
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.7 294 PEG 5000 MME, sodium acetate, Tris, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.02 39.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.881 α = 76.2 b = 45.086 β = 78.42 c = 46.915 γ = 77.17
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 4 2002-01-15 M MAD 2 1 CCD ADSC QUANTUM 4 2002-01-15
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X9A 0.9795, 0.9790, 0.9719 NSLS X9A 2 SYNCHROTRON NSLS BEAMLINE X9B 0.9715 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 2.17 18.5 95.9 0.077 0.077 12.5 2.2 14116 14116 -3 -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) 2.17 2.25 86.2 0.37 2
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) 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 MAD 2.17 18.5 14116 14116 1383 96.22 0.224 0.224 0.217 0.2674 0.284 0.2667 Random 27.251
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] -2.29 2.2 -1.8 -0.4 -2.91 3.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.237 r_scangle_it 3.068 r_scbond_it 2.124 r_angle_refined_deg 1.877 r_mcangle_it 1.088 r_mcbond_it 0.629 r_nbd_refined 0.307 r_xyhbond_nbd_refined 0.263 r_symmetry_vdw_refined 0.247 r_symmetry_hbond_refined 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.237 r_scangle_it 3.068 r_scbond_it 2.124 r_angle_refined_deg 1.877 r_mcangle_it 1.088 r_mcbond_it 0.629 r_nbd_refined 0.307 r_xyhbond_nbd_refined 0.263 r_symmetry_vdw_refined 0.247 r_symmetry_hbond_refined 0.22 r_chiral_restr 0.131 r_bond_refined_d 0.008 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2139 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling SHARP phasing