2VE6
Crystal structure of a Murine MHC class I H2-Db molecule in complex with a photocleavable peptide
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1WBX | PDB ENTRY 1WBX |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | CRYSTALS WERE GROWN AT ROOM TEMPERATURE USING THE HANGING-DROP, VAPOR-DIFFUSION METHOD WITH A WELL SOLUTION OF 15% (W/V) PEG 8000, 0.05 M K/NA PHOSPHATE, 50-100 MM BETA-OCTYL-GLUCOPYRANOSIDE AND 0.1 M CACODYLATE AT PH 6.4. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.5 | 51 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 52.24 | α = 90 |
b = 103.87 | β = 90.83 |
c = 168.81 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 CCD | 2005-03-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | APS | 19-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | ||||||||
1 | 2.65 | 20 | 96.6 | 0.08 | 9.7 | 2 | 50561 |
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 | PDB ENTRY 1WBX | 2.65 | 19.66 | 48002 | 2558 | 96.9 | 0.237 | 0.234 | 0.291 | RANDOM | 47.84 |
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] | |
0.53 | 0.92 | 2.57 | -3.07 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.274 |
r_dihedral_angle_3_deg | 14.541 |
r_dihedral_angle_4_deg | 12.842 |
r_dihedral_angle_1_deg | 5.136 |
r_angle_refined_deg | 0.895 |
r_angle_other_deg | 0.73 |
r_scangle_it | 0.372 |
r_scbond_it | 0.242 |
r_mcangle_it | 0.231 |
r_mcbond_it | 0.214 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 12628 |
Nucleic Acid Atoms | |
Solvent Atoms | 173 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |