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Human Liver Receptor Homologue DNA-Binding Domain (hLRH-1 DBD) in Complex with dsDNA from the hCYP7A1 Promoter
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CIT PDB ENTRY: 1CIT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 295 magnesium acetate, ammonium acetate, sodium cacodylate, PEG 8000, glycerol, sodium azide, hexaamine cobalt (III) trichloride, pH 6.0, hanging drop, temperature 295K, pH 6.00
Crystal Properties Matthews coefficient Solvent content 3.3 62.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.77 α = 90 b = 40.77 β = 90 c = 104.85 γ = 90
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 225 mm CCD MIRRORS 2005-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D APS 23-ID-D
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 2.2 50 99.9 0.07 27.6 5.5 8687 2 23.1
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) 2.2 2.28 100 0.441 3.2 5.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY: 1CIT 2.2 22.24 8687 8437 648 96.9 0.196 0.196 0.1975 0.226 0.2304 RANDOM 34.85
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] -0.668 -0.668 1.337
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.3 c_scangle_it 3.03 c_mcangle_it 2.25 c_scbond_it 2.03 c_mcbond_it 1.4 c_improper_angle_d 1.11 c_angle_deg 1 c_bond_d 0.005 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.3 c_scangle_it 3.03 c_mcangle_it 2.25 c_scbond_it 2.03 c_mcbond_it 1.4 c_improper_angle_d 1.11 c_angle_deg 1 c_bond_d 0.005 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 750 Nucleic Acid Atoms 486 Solvent Atoms 86 Heterogen Atoms 6
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing CNS refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling