5KRO

Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with the Methyl(phenyl)amino-substituted Estrogen, (8R,9S,13S,14S,17S)-13-methyl-17-(methyl(phenyl)amino)-7,8,9,11,12,13,14,15,16,17-decahydro-6H-cyclopenta[a]phenanthren-3-ol


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 = 54.37 α = 90
b = 81.58 β = 110.81
c = 58.37 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 -- 2013-01-31
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 1.000 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
2.08 50 98.8 0.092 -- 28.71 6.6 -- 28538 -- -- --
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)
2.08 2.12 98.3 0.606 -- -- 5.3 --

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 2.1 46.283 -- 0.0 -- 25274 1284 90.59 -- 0.197 0.1953 0.2281 --
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 2.1 2.1841 -- 94 1562 0.2437 0.2776 -- 54.0
X Ray Diffraction 2.1841 2.2835 -- 123 2478 0.2274 0.2571 -- 84.0
X Ray Diffraction 2.2835 2.4039 -- 146 2708 0.2143 0.2601 -- 93.0
X Ray Diffraction 2.4039 2.5545 -- 157 2748 0.2078 0.2362 -- 94.0
X Ray Diffraction 2.5545 2.7517 -- 137 2865 0.2152 0.2671 -- 97.0
X Ray Diffraction 2.7517 3.0286 -- 155 2893 0.2092 0.2473 -- 98.0
X Ray Diffraction 3.0286 3.4667 -- 157 2883 0.2017 0.2245 -- 98.0
X Ray Diffraction 3.4667 4.3671 -- 160 2918 0.1718 0.1815 -- 99.0
X Ray Diffraction 4.3671 46.2946 -- 155 2935 0.1785 0.227 -- 98.0
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.006
f_dihedral_angle_d 14.791
f_angle_d 0.912
f_chiral_restr 0.05
f_plane_restr 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3706
Nucleic Acid Atoms 0
Heterogen Atoms 44
Solvent Atoms 190

Software

Software
Software Name Purpose
PHENIX refinement version: (1.10.1_2155: ???)
HKL-2000 data scaling
PDB_EXTRACT data extraction version: 3.20
HKL-2000 data reduction
PHENIX phasing