5DWJ

Crystal Structure of the ER-alpha Ligand-binding Domain in Complex with a Resorcinyl 4-Fluoro-substituted Diaryl-imine analog 4-[(E)-[(4-fluorophenyl)imino](4-hydroxyphenyl)methyl]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 = 55 α = 90
b = 82.23 β = 110.37
c = 58.42 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
CCD ADSC QUANTUM 4 -- 2011-04-07
Diffraction Radiation
Monochromator Protocol
channel-cut Si(111) crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X12C 1.000 NSLS X12C

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 50 97.4 0.05 -- 26.013 3.6 -- 32176 -- -- --
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)
2.0 2.03 95.9 0.924 -- -- 3.4 1587

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 2.001 32.88 -- 0.0 -- 29137 1784 88.29 -- 0.204 0.2021 0.232 --
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 2.0006 2.0547 -- 110 1729 0.3347 0.3229 -- 72.0
X Ray Diffraction 2.0547 2.1151 -- 111 1737 0.3061 0.3543 -- 73.0
X Ray Diffraction 2.1151 2.1834 -- 100 1652 0.299 0.3199 -- 70.0
X Ray Diffraction 2.1834 2.2614 -- 140 2016 0.2713 0.2962 -- 85.0
X Ray Diffraction 2.2614 2.3519 -- 120 2017 0.2516 0.3191 -- 84.0
X Ray Diffraction 2.3519 2.4589 -- 137 2082 0.2322 0.271 -- 88.0
X Ray Diffraction 2.4589 2.5885 -- 144 2223 0.2256 0.2459 -- 93.0
X Ray Diffraction 2.5885 2.7506 -- 158 2244 0.2247 0.2505 -- 95.0
X Ray Diffraction 2.7506 2.9629 -- 156 2262 0.2226 0.2262 -- 96.0
X Ray Diffraction 2.9629 3.2608 -- 148 2333 0.2199 0.2576 -- 97.0
X Ray Diffraction 3.2608 3.7321 -- 153 2352 0.189 0.2224 -- 99.0
X Ray Diffraction 3.7321 4.6998 -- 155 2362 0.1598 0.1937 -- 99.0
X Ray Diffraction 4.6998 32.8846 -- 152 2344 0.1777 0.2062 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 57.9095
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 0.572
f_bond_d 0.002
f_chiral_restr 0.02
f_plane_restr 0.002
f_dihedral_angle_d 12.268
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3722
Nucleic Acid Atoms 0
Heterogen Atoms 48
Solvent Atoms 133

Software

Software
Software Name Purpose
HKL-2000 data scaling
PHENIX refinement
PDB_EXTRACT data extraction version: 3.15
HKL-2000 data reduction
PHENIX phasing