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Complex structure of Y.pestis virulence Factors YopN and TyeA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XKP PDB ENTRY 1XKP chain A residues 76-269
Crystallization Crystal Properties Matthews coefficient Solvent content 2.75 55.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.172 α = 90 b = 170.724 β = 90 c = 55.58 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD ADSC QUANTUM 4 2004-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 20 40229
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1XKP chain A residues 76-269 2.2 84.51 -1 38535 36265 1949 94.11 0.19461 0.19461 0.19164 0.2129 0.25036 0.2707 RANDOM 40.988
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] -3.85 -0.62 4.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.449 r_dihedral_angle_4_deg 19.139 r_dihedral_angle_3_deg 17.425 r_dihedral_angle_1_deg 6.712 r_scangle_it 4.293 r_scbond_it 2.74 r_angle_refined_deg 1.77 r_mcangle_it 1.587 r_mcbond_it 1.316 r_angle_other_deg 0.897
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.449 r_dihedral_angle_4_deg 19.139 r_dihedral_angle_3_deg 17.425 r_dihedral_angle_1_deg 6.712 r_scangle_it 4.293 r_scbond_it 2.74 r_angle_refined_deg 1.77 r_mcangle_it 1.587 r_mcbond_it 1.316 r_angle_other_deg 0.897 r_symmetry_vdw_refined 0.274 r_symmetry_hbond_refined 0.256 r_mcbond_other 0.227 r_nbd_refined 0.224 r_xyhbond_nbd_refined 0.219 r_symmetry_vdw_other 0.216 r_nbd_other 0.195 r_nbtor_refined 0.187 r_chiral_restr 0.1 r_nbtor_other 0.098 r_xyhbond_nbd_other 0.045 r_bond_refined_d 0.019 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4698 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing