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Crystal structure of RARalpha ligand binding domain in complex with the inverse agonist BMS493 and a corepressor fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DKF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 18% PEG 3350 (w/v), 0.15M NH4Cl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.46 49.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.831 α = 90 b = 105.625 β = 89.92 c = 53.382 γ = 90
Symmetry Space Group C 1 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 293 CCD ADSC QUANTUM 4 2008-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
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 43.4 0.064 0.079 13.2 2.8 32768 32768
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) 2.1 2.21 0.341 0.422 3 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1DKF 2.1 43.4 31093 1666 96.59 0.17497 0.17205 0.1713 0.22973 0.2279 RANDOM 29.592
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.314 r_dihedral_angle_4_deg 21.645 r_dihedral_angle_3_deg 14.815 r_dihedral_angle_1_deg 11.86 r_scangle_it 2.573 r_scbond_it 1.569 r_angle_refined_deg 1.216 r_mcangle_it 1.037 r_mcbond_it 0.526 r_chiral_restr 0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.314 r_dihedral_angle_4_deg 21.645 r_dihedral_angle_3_deg 14.815 r_dihedral_angle_1_deg 11.86 r_scangle_it 2.573 r_scbond_it 1.569 r_angle_refined_deg 1.216 r_mcangle_it 1.037 r_mcbond_it 0.526 r_chiral_restr 0.072 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3798 Nucleic Acid Atoms Solvent Atoms 298 Heterogen Atoms 116
Software Software Software Name Purpose ProDC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling