1BXX
MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLEXED WITH TGN38 INTERNALIZATION PEPTIDE DYQRLN
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1BW8 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.1 | 289 | HANGING DROP, 2.2M NACL, 0.4M NA/K PHOSPHATE, 10MM DTT 0.1M MES PH 7.1, 15% GLYCEROL, 16DEGREES, MOLAR RATIO OF PEPTIDE TO PROTEIN 3:1, vapor diffusion - hanging drop, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.98 | 75.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 125.26 | α = 90 |
b = 125.26 | β = 90 |
c = 73.79 | γ = 120 |
Symmetry | |
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Space Group | P 64 |
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 | MIRROR | 1998-09-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SRS BEAMLINE PX9.6 | SRS | PX9.6 |
Data Collection
Overall | |||||||||||||||||||
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ID # | 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 | |||||||
1 | 2.7 | 22 | 99.8 | 0.101 | 0.101 | 23.5 | 15.8 | 18413 | 4 | 78 |
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) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
2.7 | 2.85 | 99.8 | 0.9999999 | 0.99999 | 2.2 | 14.7 |
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 | 1BW8 | 2.7 | 22 | 18413 | 801 | 98.4 | 0.282 | 0.263 | 0.325 | RANDOM | 78 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
p_transverse_tor | 24.1 |
p_staggered_tor | 17.6 |
p_scangle_it | 5.3 |
p_scbond_it | 3.8 |
p_mcangle_it | 3.1 |
p_mcbond_it | 1.8 |
p_planar_tor | 1.7 |
p_multtor_nbd | 0.252 |
p_singtor_nbd | 0.198 |
p_xyhbond_nbd | 0.189 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2093 |
Nucleic Acid Atoms | |
Solvent Atoms | 49 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
CCP4 | data scaling |