4DMT
Crystal structure of a VWF binding collagen III derived triple helical peptide
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1V7H | 1V7H poly-ala |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 291 | 0.95-1.0 M ammonium tartrate , VAPOR DIFFUSION, HANGING DROP, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.71 | 27.99 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 31.33 | α = 90 |
b = 24.43 | β = 103.11 |
c = 39.32 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 315r | 2008-03-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | 0.975 | 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 | 1.39 | 38.29 | 99.8 | 0.107 | 13.8 | 6.9 | 11914 | 11914 | -3.7 | 8.3 |
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 | 1.39 | 1.47 | 99.6 | 0.572 | 3.8 | 6.3 | 1721 |
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 | 1V7H poly-ala | 1.39 | 38.29 | 11334 | 11334 | 570 | 99.78 | 0.10847 | 0.10671 | 0.14466 | RANDOM | 7.71 |
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] | |
-0.32 | -0.33 | -0.07 | 0.24 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.092 |
r_dihedral_angle_3_deg | 10.104 |
r_dihedral_angle_4_deg | 10.093 |
r_dihedral_angle_1_deg | 4.922 |
r_scangle_it | 3.245 |
r_scbond_it | 2.13 |
r_angle_refined_deg | 1.94 |
r_mcangle_it | 1.382 |
r_angle_other_deg | 1.002 |
r_mcbond_it | 0.921 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 606 |
Nucleic Acid Atoms | |
Solvent Atoms | 157 |
Heterogen Atoms | 24 |
Software
Software | |
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Software Name | Purpose |
XDS | data scaling |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |