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Crystal structure of putative transcriptional regulator containing a LuxR DNA binding domain (NP_811094.1) from Bacteroides thetaiotaomicron VPI-5482 at 2.04 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 NANODROP, 4.3M NaCl, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.64 66.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 233.65 α = 90 b = 233.65 β = 90 c = 125.273 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 MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2008-01-12 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162, 0.97964 SSRL BL9-2
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 2.04 48.45 100 0.095 10.2 5.63 82770 -3 36.169
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 2.04 2.11 100 0.998 1.83 5.66
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 MAD THROUGHOUT 2.04 48.45 82770 4142 99.97 0.189 0.187 0.1897 0.217 0.2203 RANDOM 35.323
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] -0.98 -0.49 -0.98 1.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.327 r_dihedral_angle_4_deg 14.475 r_dihedral_angle_3_deg 12.476 r_scangle_it 6.759 r_scbond_it 4.556 r_dihedral_angle_1_deg 4.013 r_mcangle_it 2.503 r_angle_refined_deg 1.301 r_mcbond_it 1.264 r_angle_other_deg 0.891
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.327 r_dihedral_angle_4_deg 14.475 r_dihedral_angle_3_deg 12.476 r_scangle_it 6.759 r_scbond_it 4.556 r_dihedral_angle_1_deg 4.013 r_mcangle_it 2.503 r_angle_refined_deg 1.301 r_mcbond_it 1.264 r_angle_other_deg 0.891 r_mcbond_other 0.686 r_symmetry_vdw_other 0.244 r_nbd_refined 0.2 r_nbd_other 0.192 r_symmetry_hbond_refined 0.192 r_symmetry_vdw_refined 0.186 r_metal_ion_refined 0.169 r_xyhbond_nbd_refined 0.166 r_nbtor_refined 0.165 r_nbtor_other 0.081 r_chiral_restr 0.078 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6120 Nucleic Acid Atoms Solvent Atoms 494 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction MAR345 data collection XDS data reduction SHELXD phasing autoSHARP phasing