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Crystal Structure of the Cytoplasmic domain of Yersinia Pestis YscU N263A mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JLJ PDB ENTRY 2JLJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 100 MM HEPES PH 7.5, 1 M SODIUM MALONATE PH 7.0
Crystal Properties Matthews coefficient Solvent content 2.4 47.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.873 α = 90 b = 65.873 β = 90 c = 66.677 γ = 90
Symmetry Space Group P 43 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 100 CCD MARRESEARCH 2008-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID APS 22-ID
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 1.53 50 98.4 0.05 63.4 13.5 22446 2
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 1.53 1.58 94.6 0.61 3.2 10.6
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 PDB ENTRY 2JLJ 1.53 46.88 21243 1144 98.4 0.188 0.187 0.2002 0.21 0.2199 RANDOM 20.35
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] -0.22 -0.22 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.717 r_dihedral_angle_4_deg 15.734 r_dihedral_angle_3_deg 11.521 r_dihedral_angle_1_deg 5.664 r_scangle_it 4.666 r_scbond_it 2.846 r_angle_refined_deg 1.764 r_mcangle_it 1.744 r_angle_other_deg 1.085 r_mcbond_it 0.975
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.717 r_dihedral_angle_4_deg 15.734 r_dihedral_angle_3_deg 11.521 r_dihedral_angle_1_deg 5.664 r_scangle_it 4.666 r_scbond_it 2.846 r_angle_refined_deg 1.764 r_mcangle_it 1.744 r_angle_other_deg 1.085 r_mcbond_it 0.975 r_chiral_restr 0.108 r_bond_refined_d 0.016 r_bond_other_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 907 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction SCALEPACK data scaling MOLREP phasing