4RE8

Crystal Structure of TR3 LBD in complex with Molecule 5


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION4.2277PEG4000, Sodium citrate, Glycerol, pH 4.2, vapor diffusion, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.2161.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.635α = 90
b = 76.524β = 90
c = 128.627γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmirrors2014-05-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.98SSRFBL17U

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.155070.10.057142.8174727893-3-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.1966.10.5152.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONAB INITIO PHASINGTHROUGHOUT2.1633.4626577128269.420.210980.208260.26862RANDOM46.336
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]
1.62-0.22-1.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.881
r_dihedral_angle_4_deg23.061
r_dihedral_angle_3_deg17.022
r_mcangle_it5.205
r_dihedral_angle_1_deg5.185
r_scbond_it4.464
r_mcbond_it3.877
r_mcbond_other3.873
r_angle_refined_deg1.593
r_angle_other_deg1.279
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.881
r_dihedral_angle_4_deg23.061
r_dihedral_angle_3_deg17.022
r_mcangle_it5.205
r_dihedral_angle_1_deg5.185
r_scbond_it4.464
r_mcbond_it3.877
r_mcbond_other3.873
r_angle_refined_deg1.593
r_angle_other_deg1.279
r_chiral_restr0.095
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.006
r_gen_planes_other0.006
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3607
Nucleic Acid Atoms
Solvent Atoms158
Heterogen Atoms46

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction