4ZUU

Crystal structure of Equine MHC I(Eqca-N*00602) in complexed with equine infectious anaemia virus (EIAV) derived peptide Gag-CF9


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 291.0
Details 0.02 M magnesium chloride hexahydrare, 0.1 M HEPES, 22% w/v polyacrylic acid sodium salt 5,100

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 69.47 α = 90
b = 69.47 β = 90
c = 206.46 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 ADSC QUANTUM 315r -- 2011-06-21
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 0.97900 SSRF BL17U

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 98.7 0.058 -- -- 8.8 -- 26541 -- -- --
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)
2.2 2.28 99.5 0.538 -- 4.867 9.1 --

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 2.2 31.608 -- 0.18 -- 24712 1246 92.22 -- 0.2299 0.2279 0.2664 --
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 2.1952 2.2831 -- 106 2230 0.308 0.3472 -- 80.0
X Ray Diffraction 2.2831 2.387 -- 126 2442 0.296 0.3658 -- 88.0
X Ray Diffraction 2.387 2.5128 -- 135 2481 0.275 0.342 -- 90.0
X Ray Diffraction 2.5128 2.6701 -- 153 2549 0.2895 0.2986 -- 92.0
X Ray Diffraction 2.6701 2.8761 -- 126 2650 0.2806 0.3087 -- 95.0
X Ray Diffraction 2.8761 3.1653 -- 148 2697 0.2631 0.3595 -- 96.0
X Ray Diffraction 3.1653 3.6228 -- 141 2774 0.2274 0.2569 -- 98.0
X Ray Diffraction 3.6228 4.5622 -- 161 2761 0.1864 0.2178 -- 96.0
X Ray Diffraction 4.5622 31.6114 -- 150 2882 0.192 0.2223 -- 94.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 7.894
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 7.894
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -15.7879
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.008
f_plane_restr 0.004
f_angle_d 0.853
f_dihedral_angle_d 19.122
f_chiral_restr 0.068
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3116
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 130

Software

Software
Software Name Purpose
PHENIX refinement version: 1.5_2
HKL-2000 data reduction
HKL-2000 data scaling
HKL-2000 phasing