4DMU
Crystal structure of the von Willebrand factor A3 domain in complex with a collagen III derived triple-helical peptide
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 277 | 100 mM cacodylate, pH 6.5, 1.20 M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.69 | 54.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 187.614 | α = 90 |
b = 187.614 | β = 90 |
c = 89.373 | γ = 120 |
Symmetry | |
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Space Group | P 6 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315r | 2006-10-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | 0.9395 | 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 | 2.8 | 46.9 | 92.5 | 0.081 | 14.9 | 7 | 41019 | 41019 | 3 | 67.3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.8 | 2.95 | 73.1 | 0.452 | 2.3 | 3 | 4679 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1ATZ & 4DMT | 2.8 | 46.32 | 38880 | 38880 | 2090 | 92.23 | 0.20416 | 0.20154 | 0.2531 | RANDOM - not-related by twinning | 46.995 |
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] | |
-19.75 | -19.75 | 39.5 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.892 |
r_dihedral_angle_3_deg | 18.633 |
r_dihedral_angle_4_deg | 18.266 |
r_dihedral_angle_1_deg | 6.512 |
r_angle_refined_deg | 1.649 |
r_scangle_it | 1.379 |
r_angle_other_deg | 0.922 |
r_scbond_it | 0.897 |
r_mcangle_it | 0.433 |
r_mcbond_it | 0.26 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11631 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 20 |
Software
Software | |
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Software Name | Purpose |
XDS | data scaling |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |