5AAU

Optimization of a novel binding motif to to (E)-3-(3,5-difluoro-4-((1R,3R)-2-(2-fluoro-2-methylpropyl)-3-methyl-2,3,4,9-tetrahydro-1H- pyrido(3,4-b)indol-1-yl)phenyl)acrylic acid (AZD9496), a potent and orally bioavailable selective estrogen receptor downregulator and antagonist


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherIN HOUSE MODEL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.50.1 M PCTP, PH 6.5 (0.04 M SODIUM PROPIONATE, 0.02 M SODIUM CACODYLATE, 0.04 M BIS-TRIS PROPANE), 22% PEG3350, 0.2M MGCL2
Crystal Properties
Matthews coefficientSolvent content
2.0740.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.407α = 90
b = 51.396β = 93.66
c = 85.181γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04DiamondI04

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
11.985910.0415.33.3314542
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)
11.9257.30.481.82.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTIN HOUSE MODEL1.925.731453162990.920.175510.172930.22591RANDOM28.396
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]
0.18-0.02-0.510.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.298
r_dihedral_angle_4_deg21.983
r_dihedral_angle_3_deg15.451
r_dihedral_angle_1_deg5.945
r_mcangle_it2.734
r_scbond_it2.389
r_angle_refined_deg2.104
r_mcbond_it1.803
r_mcbond_other1.791
r_angle_other_deg1.149
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.298
r_dihedral_angle_4_deg21.983
r_dihedral_angle_3_deg15.451
r_dihedral_angle_1_deg5.945
r_mcangle_it2.734
r_scbond_it2.389
r_angle_refined_deg2.104
r_mcbond_it1.803
r_mcbond_other1.791
r_angle_other_deg1.149
r_chiral_restr0.137
r_bond_refined_d0.024
r_gen_planes_refined0.012
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms3532
Nucleic Acid Atoms
Solvent Atoms227
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing