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The crystal structure of the full-length transcriptional regulator LuxT from Vibrio parahaemolyticus RIMD 2210633.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1M MES,
12% PEG 20000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.02 69.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.792 α = 90 b = 89.792 β = 90 c = 125.028 γ = 120
Symmetry Space Group P 32 2 1
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 mirror 2008-07-27 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97929, 0.97944 APS 19-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 3.2 45 99.7 0.143 24.5 6.5 10042 10042
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 3.2 3.25 100 0.74 2.67 5.8 981
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 3.2 44.9 9531 9531 483 99.7 0.22498 0.22498 0.22306 0.2208 0.26112 0.2638 RANDOM 48.216
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] 1.24 0.62 1.24 -1.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.434 r_dihedral_angle_3_deg 24.535 r_dihedral_angle_4_deg 20.035 r_dihedral_angle_1_deg 7.023 r_scangle_it 3.04 r_angle_refined_deg 1.777 r_scbond_it 1.748 r_mcangle_it 1.056 r_mcbond_it 0.542 r_chiral_restr 0.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.434 r_dihedral_angle_3_deg 24.535 r_dihedral_angle_4_deg 20.035 r_dihedral_angle_1_deg 7.023 r_scangle_it 3.04 r_angle_refined_deg 1.777 r_scbond_it 1.748 r_mcangle_it 1.056 r_mcbond_it 0.542 r_chiral_restr 0.117 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 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 2372 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 24
Software Software Software Name Purpose SBC-Collect data collection SHELXD phasing MLPHARE phasing DM model building RESOLVE model building HKL-3000 phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling DM phasing RESOLVE phasing