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Crystal structure of a LacI family transcriptional regulator from Silicibacter pomeroyi
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 294 100mM Hepes pH 7.0, 20% PEG 3350, 200mM sodium chloride, Vapor diffusion, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.03 39.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.4 α = 82.91 b = 60.443 β = 76.96 c = 90.766 γ = 87.22
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 MAR CCD 165 mm 2008-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97958 APS 31-ID
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 1.6 87.833 95.5 0.091 0.091 12.1 3.9 163765 156396 16.3
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) 1.6 1.69 93.8 0.502 0.502 2.1 3.9 22479
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 (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 1.6 15 163574 156311 7876 95.56 0.185 0.184 0.1879 0.215 0.2171 RANDOM 22.032
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] -0.16 0.1 -0.11 -0.29 0.03 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.643 r_dihedral_angle_4_deg 20.523 r_dihedral_angle_3_deg 13.309 r_dihedral_angle_1_deg 5.085 r_scangle_it 3.321 r_scbond_it 2.182 r_angle_refined_deg 1.293 r_mcangle_it 1.26 r_mcbond_it 0.781 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.643 r_dihedral_angle_4_deg 20.523 r_dihedral_angle_3_deg 13.309 r_dihedral_angle_1_deg 5.085 r_scangle_it 3.321 r_scbond_it 2.182 r_angle_refined_deg 1.293 r_mcangle_it 1.26 r_mcbond_it 0.781 r_nbtor_refined 0.311 r_nbd_refined 0.195 r_symmetry_hbond_refined 0.146 r_symmetry_vdw_refined 0.141 r_xyhbond_nbd_refined 0.123 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8441 Nucleic Acid Atoms Solvent Atoms 1036 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction SHELXCD phasing SHELXE model building