4WPC
Crystal structure of Rgd1p F-BAR domain in complex with inositol phosphate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4WPE | PDB ENTRY 4WPE |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 294 | 0.1 M citrate, pH 5.5, containing 0.1-0.2 M (NH4)2SO4 plus 10-20% (w/v) PEG3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.61 | 73.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 178.993 | α = 90 |
b = 74.11 | β = 104.27 |
c = 105.734 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 QUANTUM 270 | 2007-11-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CHESS BEAMLINE F1 | 0.91790 | CHESS | F1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 3.3 | 50 | 99.7 | 14 | 4.2 | 19341 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | PDB ENTRY 4WPE | 3.34 | 30.773 | 1.33 | 19300 | 993 | 97.87 | 0.2632 | 0.2613 | 0.3 |
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 |
f_dihedral_angle_d | 16.175 |
f_angle_d | 1.115 |
f_chiral_restr | 0.459 |
f_bond_d | 0.01 |
f_plane_restr | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4306 |
Nucleic Acid Atoms | |
Solvent Atoms | 8 |
Heterogen Atoms | 72 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
PHASER | phasing |
HKL-2000 | data scaling |