2XI7
N-terminal endonuclease domain of La Crosse virus L-protein
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2XI5 | PDB ENTRY 2XI5 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.5 | 15-20 MG/ML PROTEIN IN 20 MM HEPES PH 7.5 150 MM NACL 5MM MNCL2 AND 2.5 MM BETA-MERCAPTO-ETHANOL AND A RESERVOIR COMPOSITION OF 3.4 M NA-FORMATE 0.1 M TRIS-HCL PH 8 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4 | 69.2 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 124.59 | ¦Á = 90 |
b = 124.59 | ¦Â = 90 |
c = 294.71 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 61 2 2 |
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 | 2009-11-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | ESRF | ID29 |
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 | 2.2 | 50 | 100 | 0.08 | 23.4 | 14.3 | 69332 |
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 | 2.2 | 2.28 | 100 | 0.59 | 5.1 | 14.6 |
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 2XI5 | 2.2 | 47.29 | 66523 | 2787 | 100 | 0.19 | 0.188 | 0.221 | RANDOM | 26.06 |
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] | |
0.48 | 0.24 | 0.48 | -0.72 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.52 |
r_dihedral_angle_3_deg | 15.021 |
r_dihedral_angle_4_deg | 14.741 |
r_dihedral_angle_1_deg | 5.477 |
r_scangle_it | 4.883 |
r_scbond_it | 2.884 |
r_mcangle_it | 1.886 |
r_angle_refined_deg | 1.556 |
r_mcbond_it | 0.958 |
r_angle_other_deg | 0.932 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6116 |
Nucleic Acid Atoms | |
Solvent Atoms | 445 |
Heterogen Atoms | 64 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |