4DLD

Crystal structure of the GluK1 ligand-binding domain (S1S2) in complex with the antagonist (S)-2-amino-3-(2-(2-carboxyethyl)-5-chloro-4-nitrophenyl)propionic acid at 2.0 A resolution



X-RAY DIFFRACTION Experimental Data & Validation

X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 279.0
Details 17 % PEG4000, 0.1M cacodylic acid, 0.3M lithium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 69.32 α = 90
b = 69.32 β = 90
c = 234.97 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- 2010-03-19
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MAX II BEAMLINE I911-2 1.0380 MAX_II I911-2

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 25.88 99.9 -- 0.081 -- 7.9 39813 39813 -- -- 21.09
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 2.11 100.0 0.318 0.318 1.8 8.0 5696

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 2.0 25.877 -- 1.35 -- 39768 1997 99.83 -- 0.1894 0.1864 0.246 Random
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 2.0 2.05 2656 139 2656 0.2213 0.2943 -- 100.0
X Ray Diffraction 2.05 2.1054 2622 142 2622 0.2016 0.279 -- 100.0
X Ray Diffraction 2.1054 2.1674 2662 145 2662 0.1953 0.2654 -- 100.0
X Ray Diffraction 2.1674 2.2373 2671 127 2671 0.1804 0.2427 -- 100.0
X Ray Diffraction 2.2373 2.3172 2671 109 2671 0.192 0.2561 -- 100.0
X Ray Diffraction 2.3172 2.4099 2639 157 2639 0.1952 0.275 -- 100.0
X Ray Diffraction 2.4099 2.5195 2646 152 2646 0.1995 0.2806 -- 100.0
X Ray Diffraction 2.5195 2.6522 2684 160 2684 0.1975 0.2801 -- 100.0
X Ray Diffraction 2.6522 2.8182 2685 133 2685 0.205 0.2661 -- 100.0
X Ray Diffraction 2.8182 3.0355 2723 123 2723 0.198 0.2475 -- 100.0
X Ray Diffraction 3.0355 3.3404 2700 145 2700 0.1878 0.2369 -- 100.0
X Ray Diffraction 3.3404 3.8224 2726 157 2726 0.1774 0.2503 -- 100.0
X Ray Diffraction 3.8224 4.8108 2757 163 2757 0.1507 0.202 -- 100.0
X Ray Diffraction 4.8108 25.8796 2929 145 2929 0.1907 0.22 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Restrained
Mean Isotropic B 24.6097
Anisotropic B[1][1] 2.019
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.019
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.038
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.384
f_chiral_restr 0.069
f_bond_d 0.007
f_angle_d 1.035
f_plane_restr 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4058
Nucleic Acid Atoms 0
Heterogen Atoms 54
Solvent Atoms 501

Software

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling version: 3.3.9
PHASER phasing
PHENIX refinement version: 1.7.1_743
PDB_EXTRACT data extraction version: 3.10