3G2U
VHS Domain of human GGA1 complexed with Sotilin C-terminal Peptide
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1JWF |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6 | 292 | 15%(w/v) PEG 5000 mmE, 0.2M NH4I, 0.3M 1,6-hexanediol, 0.1M MES-NaOH, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.48 | 50.37 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 48.486 | α = 90 |
b = 72.728 | β = 90 |
c = 103.767 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | IMAGE PLATE | MAR scanner 345 mm plate | 2007-03-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE BW7B | 0.8423 | EMBL/DESY, HAMBURG | BW7B |
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 | 2.3 | 43.5 | 99 | 0.081 | 15.3 | 5.66 | 16852 | 16683 | -3 | -3 | 34.1 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.3 | 2.4 | 99.6 | 0.349 | 4.4 | 5.17 | 2428 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | 1JWF | 2.301 | 37.601 | 16852 | 16629 | 836 | 98.4 | 0.201 | 0.199 | 0.246 | RANDOM | 41.418 |
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] | |
3.895 | 0.182 | -4.077 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 22.253 |
f_angle_d | 0.986 |
f_chiral_restr | 0.081 |
f_plane_restr | 0.017 |
f_bond_d | 0.009 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2366 |
Nucleic Acid Atoms | |
Solvent Atoms | 147 |
Heterogen Atoms | 5 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
XDS | data scaling |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |