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Crystal Structure of the RARbeta/RXRalpha Ligand Binding Domain Heterodimer in Complex with 9-cis Retinoic Acid and a Fragment of the TRAP220 Coactivator
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DKF TRUNCATED VERSION OF PDB ENTRY 1DKF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 291 PEG 3350, Sodium Formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 7.50
Crystal Properties Matthews coefficient Solvent content 3.6 65.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.7 α = 90 b = 115.7 β = 90 c = 247.2 γ = 120
Symmetry Space Group P 31 2 1
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 MARRESEARCH 2003-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.9 36.21 99.7 0.083 5.2 7.4 42989 92
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.06 99.6 0.38 2 7.5
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 TRUNCATED VERSION OF PDB ENTRY 1DKF 2.9 30 43207 42989 1372 99.6 0.253 0.253 0.2534 0.296 0.2921 RANDOM 73.3
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] 15.57 14.54 15.57 -31.14
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.9 c_angle_deg 1.87 c_improper_angle_d 1.25 c_bond_d 0.014 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.9 c_angle_deg 1.87 c_improper_angle_d 1.25 c_bond_d 0.014 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 c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7582 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 88
Software Software Software Name Purpose MAR345 data collection SCALA data scaling MOLREP phasing CNS refinement MOSFLM data reduction CCP4 data scaling