2VSM
Nipah virus attachment glycoprotein in complex with human cell surface receptor ephrinB2
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 5.6 | 18% ISOPROPANOL, 18% PEG 3350 AND 0.1 M TRI-CITRATE BUFFER PH 5.6 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.3 | 46 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 63.236 | ¦Á = 90 |
b = 95.834 | ¦Â = 90 |
c = 97.909 | ¦Ã = 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 | 77.2 | CCD | ADSC CCD | MIRRORS | 2006-12-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-2 | ESRF | ID14-2 |
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 | 1.8 | 30 | 98.9 | 0.09 | 15 | 6.9 | 55159 | -3 |
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 | 1.8 | 1.86 | 90.4 | 0.52 | 2.3 | 5.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | PDB ENTRY 1NUK AND 1V3E | 1.8 | 30 | 52300 | 2800 | 98.8 | 0.154 | 0.152 | 0.198 | RANDOM | 11.79 |
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] | |
0.14 | 0.02 | -0.16 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.58 |
r_dihedral_angle_4_deg | 13.405 |
r_dihedral_angle_1_deg | 12.687 |
r_dihedral_angle_3_deg | 12.266 |
r_scangle_it | 7 |
r_scbond_it | 5.178 |
r_mcangle_it | 3.58 |
r_mcbond_it | 3.2 |
r_angle_refined_deg | 1.532 |
r_angle_other_deg | 0.939 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4373 |
Nucleic Acid Atoms | |
Solvent Atoms | 705 |
Heterogen Atoms | 60 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |