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Crystal structure of CviR ligand-binding domain bound to the native ligand C6-HSL
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QP6 PDB ENTRY 3QP6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 9 296 100 mM Tris-Cl, 200 mM magnesium chloride, 25-35% w/v PEG3350, pH 9.0, VAPOR DIFFUSION, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.39 48.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.543 α = 90 b = 55.973 β = 90 c = 125.223 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 CCD ADSC QUANTUM 315 2010-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.55 62.622 96 0.046 11 28892 28173 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) 1.55 1.61 96 0.476 2.536 7.9
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 3QP6 1.55 62.62 28173 26749 1423 97.51 0.21681 0.21681 0.21519 0.2204 0.24735 0.254 RANDOM 29.393
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 0.51 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.671 r_dihedral_angle_4_deg 13.002 r_dihedral_angle_3_deg 12.935 r_dihedral_angle_1_deg 4.566 r_scangle_it 3.567 r_scbond_it 2.279 r_mcangle_it 1.666 r_angle_refined_deg 1.234 r_mcbond_it 1.034 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.671 r_dihedral_angle_4_deg 13.002 r_dihedral_angle_3_deg 12.935 r_dihedral_angle_1_deg 4.566 r_scangle_it 3.567 r_scbond_it 2.279 r_mcangle_it 1.666 r_angle_refined_deg 1.234 r_mcbond_it 1.034 r_nbtor_refined 0.305 r_symmetry_hbond_refined 0.267 r_symmetry_vdw_refined 0.237 r_nbd_refined 0.211 r_xyhbond_nbd_refined 0.178 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 1403 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 14
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling