2VCP
Crystal structure of N-Wasp VC domain in complex with skeletal actin
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2A3Z | PDB ENTRY 2A3Z |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 7 | 277 | VAPOR DIFFUSION METHOD (4 C) PROTEIN SOLUTION: 0.18MM ACTIN, 0.36MM N-WASP PEPTIDE, 5MM TRIS.HCL PH7.0, ATP 0.2MM, CACL2 0.02MM, TCEP 20MM, NAN3 0.01%. RESERVOIR: 10.2% (V/V) TACSIMATE, 13.2%(W/V)PEG 8000, 100MM HEPES PH7.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
5.2 | 76.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 136.24 | α = 90 |
b = 136.24 | β = 90 |
c = 205.41 | γ = 120 |
Symmetry | |
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Space Group | P 61 |
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 | DOUBLE CRYSTAL, SI(111) | 2006-12-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | ESRF | ID14-4 |
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 | 3.2 | 48.3 | 98.5 | 0.12 | 8.8 | 3.5 | 35056 | 35.9 |
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 | 3.2 | 3.37 | 95 | 0.4 | 2.3 | 2.3 |
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 | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2A3Z | 3.2 | 20 | 3 | 32407 | 1453 | 91.4 | 0.275 | 0.275 | 0.331 | RANDOM | 28.6 |
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] | |
-2.07 | -6.5 | -2.07 | 5.42 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 23.2 |
c_angle_deg | 1.6 |
c_improper_angle_d | 1.01 |
c_bond_d | 0.011 |
c_bond_d_na | |
c_bond_d_prot | |
c_angle_d | |
c_angle_d_na | |
c_angle_d_prot | |
c_angle_deg_na |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6092 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 64 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
AMoRE | phasing |