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Crystal structure of CviR ligand-binding domain bound to C10-HSL
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PQ1 PDB ENTRY 3PQ1
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 2.38 48.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.196 α = 90 b = 56.216 β = 90 c = 124.944 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 2009-02-27 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 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 1.55 62.472 99.9 0.041 0.041 24.987 6.9 28620 28565 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 99.9 0.36 4.024 5.3
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 (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 3PQ1 1.55 62.47 27121 1444 99.85 0.2103 0.2103 0.20885 0.2117 0.23797 0.2446 RANDOM 27.787
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] 0.34 0.22 -0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.914 r_dihedral_angle_4_deg 13.315 r_dihedral_angle_3_deg 12.827 r_dihedral_angle_1_deg 4.68 r_scangle_it 3.406 r_scbond_it 2.167 r_mcangle_it 1.526 r_angle_refined_deg 1.217 r_mcbond_it 0.969 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.914 r_dihedral_angle_4_deg 13.315 r_dihedral_angle_3_deg 12.827 r_dihedral_angle_1_deg 4.68 r_scangle_it 3.406 r_scbond_it 2.167 r_mcangle_it 1.526 r_angle_refined_deg 1.217 r_mcbond_it 0.969 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.241 r_nbd_refined 0.206 r_xyhbond_nbd_refined 0.148 r_symmetry_hbond_refined 0.129 r_chiral_restr 0.08 r_bond_refined_d 0.009 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 138 Heterogen Atoms 18
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling