3KMR

Crystal structure of RARalpha ligand binding domain in complex with an agonist ligand (Am580) and a coactivator fragment


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DKFPDB ENTRY 1DKF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529315% (w/v) PEG 6000, 5% (w/v) glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1939.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.307α = 90
b = 61.218β = 105.38
c = 49.444γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 315r2008-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.9395ESRFID14-2

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.8350.030.04316.22.6221722217225.51
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)RedundancyNumber Unique Reflections (All)
1.81.90.2260.3193.62.52665

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1DKF1.832.02221722145272093.780.198750.197440.23716RANDOM29.809
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]
-0.43-0.840.19-0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.712
r_dihedral_angle_4_deg18.519
r_dihedral_angle_3_deg14.83
r_dihedral_angle_1_deg4.469
r_scangle_it2.771
r_angle_refined_deg2.7
r_scbond_it1.75
r_mcangle_it0.98
r_mcbond_it0.49
r_chiral_restr0.073
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.712
r_dihedral_angle_4_deg18.519
r_dihedral_angle_3_deg14.83
r_dihedral_angle_1_deg4.469
r_scangle_it2.771
r_angle_refined_deg2.7
r_scbond_it1.75
r_mcangle_it0.98
r_mcbond_it0.49
r_chiral_restr0.073
r_bond_refined_d0.01
r_gen_planes_refined0.005
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 AtomsNumber
Protein Atoms1937
Nucleic Acid Atoms
Solvent Atoms121
Heterogen Atoms26

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling