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Crystal structure of the master transcriptional regulator, SmcR, in Vibrio vulnificus provides insight into its DNA recognition mechanism
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 294 0.2M Lithium sulfate, 7% PEG 3000, 0.1M imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.61 52.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.494 α = 90 b = 99.025 β = 90 c = 129.06 γ = 90
Symmetry Space Group P 21 21 21
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 210 2006-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 6C1 1.23985 PAL/PLS 6C1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.1 35 99.2 0.072 0.047 26.97 6.9 59111 56004 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.18 95.6 0.475 0.393 3.28 6.2 5617
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.1 29.92 2 2 59111 56004 2979 99.16 0.212 0.20033 0.19759 0.25095 0.2437 RANDOM 35.58
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] -1.94 2.63 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.816 r_dihedral_angle_4_deg 16.911 r_dihedral_angle_3_deg 16.342 r_dihedral_angle_1_deg 5.284 r_scangle_it 3.629 r_scbond_it 2.471 r_mcangle_it 1.484 r_angle_refined_deg 1.329 r_mcbond_it 0.978 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.816 r_dihedral_angle_4_deg 16.911 r_dihedral_angle_3_deg 16.342 r_dihedral_angle_1_deg 5.284 r_scangle_it 3.629 r_scbond_it 2.471 r_mcangle_it 1.484 r_angle_refined_deg 1.329 r_mcbond_it 0.978 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.282 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.185 r_symmetry_hbond_refined 0.172 r_chiral_restr 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6560 Nucleic Acid Atoms Solvent Atoms 453 Heterogen Atoms 30
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling