4DJ9
Human vinculin head domain Vh1 (residues 1-258) in complex with the talin vinculin binding site 50 (VBS50, residues 2078-2099)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 7.5 | The human vinculin Vh1 domain (residues 1 - 258) was generated as described.9 Crystallization screens of Vh1 protein and VBS50 mixed in 1:5 molar ratio were performed at two temperatures. Co-crystals were obtained from Hampton crystal screen I with a reservoir of 0.1 M Hepes pH 7.5, 10% w/v polyethylene glycol 6,000, and 5% 2-Methyl-2,4-pentanediol. Crystals were transferred directly from the initial 96-well screening plate into Paratone-N oil and flash-frozen in liquid nitrogen. , VAPOR DIFFUSION |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.47 | 50.25 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 33.54 | α = 90 |
b = 68.16 | β = 90 |
c = 137.6 | 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 | CCD | RAYONIX MX-300 | 2009-08-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 1.0 | APS | 22-ID |
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 | 2.25 | 68.8 | 99.7 | 0.065 | 0.065 | 16.4 | 7 | 15637 | 55.65 |
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) | ||||||||||
1 | 2.251 | 2.258 | 100 | 0.592 | 0.592 | 3.3 | 7.2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 2.25 | 68.8 | 15586 | 787 | 99.32 | 0.2095 | 0.2076 | 0.2472 | RANDOM | 70.73 |
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] | |
-15.5041 | -3.5916 | 19.0957 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 17.64 |
t_omega_torsion | 2.15 |
t_angle_deg | 1.12 |
t_bond_d | 0.01 |
t_dihedral_angle_d | |
t_incorr_chiral_ct | |
t_pseud_angle | |
t_trig_c_planes | |
t_gen_planes | |
t_it |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2017 |
Nucleic Acid Atoms | |
Solvent Atoms | 62 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
BUSTER | refinement |
autoPROC | data scaling |
XDS | data reduction |
SCALA | data scaling |