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LytTr DNA-binding domain of putative methyl-accepting/DNA response regulator from Bacillus cereus.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 0.4 M magnesium chloride, 0.1 M HEPES buffer.
Full length protein consisting of 214 original residues was used for crystallization. The obtained crystals contain only C-terminal domain of the protein, probably, due to proteolysis of the protein in crystallization conditions. , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.86 56.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.784 α = 90 b = 88.784 β = 90 c = 74.425 γ = 90
Symmetry Space Group P 42 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 100 CCD ADSC QUANTUM 315 2008-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9792 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 2.4 48 100 0.073 13.6 27.8 12166 12166 65.6
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 2.4 2.44 100 0.913 4.4 26.7 583
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 SAD THROUGHOUT 2.4 48 12141 12141 581 99.93 0.184 0.184 0.182 0.189 0.209 0.2182 RANDOM 50.238
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] 0.43 0.43 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.831 r_dihedral_angle_3_deg 20.146 r_dihedral_angle_4_deg 15.267 r_dihedral_angle_1_deg 7.001 r_scangle_it 3.263 r_scbond_it 2.222 r_mcangle_it 1.701 r_angle_refined_deg 1.664 r_mcbond_it 1.348 r_angle_other_deg 0.984
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.831 r_dihedral_angle_3_deg 20.146 r_dihedral_angle_4_deg 15.267 r_dihedral_angle_1_deg 7.001 r_scangle_it 3.263 r_scbond_it 2.222 r_mcangle_it 1.701 r_angle_refined_deg 1.664 r_mcbond_it 1.348 r_angle_other_deg 0.984 r_nbd_refined 0.213 r_nbd_other 0.207 r_symmetry_vdw_other 0.207 r_symmetry_hbond_refined 0.194 r_nbtor_refined 0.19 r_mcbond_other 0.189 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.099 r_nbtor_other 0.095 r_symmetry_vdw_refined 0.08 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1778 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 12
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction SHELXD phasing MLPHARE phasing DM phasing SOLVE phasing RESOLVE phasing HKL-3000 phasing