5TLF

Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with the Constrained WAY Derivative, 4-(2-(3-methylbut-2-en-1-yl)-7-(trifluoromethyl)-2H-indazol-3-yl)benzene-1,3-diol


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.3
Temperature 294.0
Details 15% PEG 3350, 0.05M MgCl2, 0.067M NaCl, 0.1M Tris

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.65 α = 90
b = 81.57 β = 109.96
c = 58.65 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2014-01-24
Diffraction Radiation
Monochromator Protocol
Side scattering bent cube i-beam single crystal asymmetric cut 4.965 degs SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.979 SSRL BL11-1

Data Collection

Overall
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
2.2 50 97.9 0.096 -- 17.943 3.4 -- 23906 -- -- 35.92
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.21 2.25 98.8 0.459 -- -- 3.4 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 2.204 46.28 -- 0.0 -- 22831 1932 93.14 -- 0.1912 0.1878 0.2291 --
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.2044 2.2595 -- 128 1289 0.2701 0.3109 -- 81.0
X Ray Diffraction 2.2595 2.3206 -- 134 1354 0.2298 0.2529 -- 86.0
X Ray Diffraction 2.3206 2.3889 -- 128 1467 0.2259 0.2805 -- 92.0
X Ray Diffraction 2.3889 2.466 -- 153 1463 0.2118 0.2882 -- 92.0
X Ray Diffraction 2.466 2.5541 -- 133 1488 0.2068 0.2832 -- 93.0
X Ray Diffraction 2.5541 2.6564 -- 141 1473 0.216 0.2659 -- 93.0
X Ray Diffraction 2.6564 2.7773 -- 120 1462 0.2116 0.2556 -- 91.0
X Ray Diffraction 2.7773 2.9237 -- 147 1488 0.203 0.28 -- 93.0
X Ray Diffraction 2.9237 3.1068 -- 136 1557 0.1988 0.2386 -- 97.0
X Ray Diffraction 3.1068 3.3466 -- 139 1571 0.2062 0.2696 -- 98.0
X Ray Diffraction 3.3466 3.6833 -- 143 1581 0.181 0.2345 -- 98.0
X Ray Diffraction 3.6833 4.216 -- 137 1518 0.1602 0.189 -- 95.0
X Ray Diffraction 4.216 5.3104 -- 150 1593 0.1578 0.1756 -- 99.0
X Ray Diffraction 5.3104 46.29 -- 143 1595 0.1784 0.2098 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 47.7181
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_dihedral_angle_d 16.079
f_bond_d 0.005
f_angle_d 0.921
f_chiral_restr 0.039
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3849
Nucleic Acid Atoms 0
Heterogen Atoms 52
Solvent Atoms 161

Software

Software
Software Name Purpose
PHENIX refinement version: 1.10.1_2155
PDB_EXTRACT data extraction version: 3.20
HKL-2000 data scaling
HKL-2000 data reduction
PHENIX phasing
DENZO data reduction
SCALEPACK data scaling