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Crystal structure of LsrB from Yersinia pestis complexed with autoinducer-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TJY PDB ENTRY 1TJY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 Qiagen PEG Suite condition number 92: 20% PEG3350, 200 mM di-ammonium phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.13 42.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.613 α = 90 b = 61.033 β = 90 c = 125.231 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ Osmic Blue 2008-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
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 1.75 62.62 98.9 0.049 23.3 6.5 31947 31947 2 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 1.75 1.84 93.7 0.261 6.5 5.7 4339
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1TJY 1.75 19.749 30271 30271 1618 98.91 0.18176 0.18176 0.18 0.1787 0.2128 0.2109 RANDOM 17.389
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] 0.21 0.06 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.04 r_dihedral_angle_4_deg 16.026 r_dihedral_angle_3_deg 13.636 r_dihedral_angle_1_deg 6.078 r_scangle_it 3.614 r_scbond_it 2.168 r_angle_refined_deg 1.361 r_mcangle_it 1.296 r_mcbond_it 0.701 r_chiral_restr 0.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.04 r_dihedral_angle_4_deg 16.026 r_dihedral_angle_3_deg 13.636 r_dihedral_angle_1_deg 6.078 r_scangle_it 3.614 r_scbond_it 2.168 r_angle_refined_deg 1.361 r_mcangle_it 1.296 r_mcbond_it 0.701 r_chiral_restr 0.103 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2398 Nucleic Acid Atoms Solvent Atoms 380 Heterogen Atoms 10
Software Software Software Name Purpose StructureStudio data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling