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Crystal structure of a LuxT domain from Vibrio parahaemolyticus RIMD 2210633
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 0.1M Bis-tris propane, 1.3M di-Ammonium tartrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 4.58 73.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.438 α = 90 b = 147.438 β = 90 c = 382.487 γ = 120
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 Mirrors 2007-10-06 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97935, 0.97948 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 3.1 48.22 99.8 0.123 23.3 7.4 29395 29395 85.8
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) 3.1 3.19 100 0.756 2.9 7.3 2453
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 3.1 48.22 27890 27890 1490 99.79 0.19237 0.19237 0.19019 0.1882 0.23218 0.2324 RANDOM 69.169
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.684 r_dihedral_angle_3_deg 24.239 r_dihedral_angle_4_deg 19.925 r_dihedral_angle_1_deg 6.505 r_mcangle_it 2.42 r_scangle_it 2.137 r_angle_refined_deg 1.802 r_mcbond_it 1.392 r_scbond_it 1.287 r_nbtor_refined 0.333
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.684 r_dihedral_angle_3_deg 24.239 r_dihedral_angle_4_deg 19.925 r_dihedral_angle_1_deg 6.505 r_mcangle_it 2.42 r_scangle_it 2.137 r_angle_refined_deg 1.802 r_mcbond_it 1.392 r_scbond_it 1.287 r_nbtor_refined 0.333 r_nbd_refined 0.262 r_symmetry_vdw_refined 0.197 r_symmetry_hbond_refined 0.142 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.123 r_bond_refined_d 0.018 r_gen_planes_refined 0.005 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 5906 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling SHELXS phasing MLPHARE phasing DM phasing HKL-3000 phasing