4PGD
MHC Class I in complex with modified Sendai virus nucleoprotein peptide FAPGNYPAF
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | sodium/potassium phosphate buffer 1.9M, MPD 1%, glycerol (cryoprotection) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.85 | 56.88 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 88.047 | α = 90 |
b = 137.027 | β = 90 |
c = 45.184 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315r | 2012-05-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 1.0000 | ESRF | ID23-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | 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 | ||||||
1 | 2.7 | 74.074 | 99.7 | 0.139 | 0.162 | 0.082 | 10.6 | 3.8 | 15630 | 15630 | 39.42 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.7 | 2.85 | 99.6 | 0.55 | 0.55 | 0.321 | 1.3 | 3.9 | 2245 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2VAB | 2.7 | 45.22 | 15605 | 773 | 99.5 | 0.213 | 0.21 | 0.259 | RANDOM | 29.81 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.55 | 0.97 | -0.43 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.401 |
r_dihedral_angle_3_deg | 12.521 |
r_dihedral_angle_4_deg | 10.614 |
r_dihedral_angle_1_deg | 5.385 |
r_mcangle_it | 3.028 |
r_mcbond_it | 1.714 |
r_mcbond_other | 1.712 |
r_angle_refined_deg | 0.926 |
r_angle_other_deg | 0.662 |
r_chiral_restr | 0.057 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3123 |
Nucleic Acid Atoms | |
Solvent Atoms | 15 |
Heterogen Atoms | 6 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SCALA | data scaling |
XDS | data scaling |
Coot | model building |
PDB_EXTRACT | data extraction |