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Crystal structure of Vibrio harveyi LuxQ periplasmic domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 296 1:3 mixture of protein (10 mg/ml in 10 mM Tris-HCl, 150 mM NaCl, pH 7.5) and well solution (8% (w/v) PEG 2000 monomethyl ether (MME), 10 mM Tris-HCl (pH 7.0), and 10 mM NiCl2), VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.18 43.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.446 α = 82.18 b = 36.152 β = 86.14 c = 49.185 γ = 67.28
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 ADSC QUANTUM 315 2005-07-29 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) 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 1.7 30 92.7 21488
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.7 1.76 85.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.7 26.1 20385 1102 92.75 0.19659 0.19433 0.1952 0.23709 0.2358 RANDOM 21.363
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] 0.35 -0.09 0.03 -0.8 1.01 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.326 r_dihedral_angle_4_deg 19.176 r_dihedral_angle_3_deg 15.255 r_dihedral_angle_1_deg 5.46 r_scangle_it 3.467 r_scbond_it 2.352 r_mcangle_it 1.577 r_angle_refined_deg 1.348 r_mcbond_it 0.915 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.326 r_dihedral_angle_4_deg 19.176 r_dihedral_angle_3_deg 15.255 r_dihedral_angle_1_deg 5.46 r_scangle_it 3.467 r_scbond_it 2.352 r_mcangle_it 1.577 r_angle_refined_deg 1.348 r_mcbond_it 0.915 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.248 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.15 r_symmetry_hbond_refined 0.102 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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 1665 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing