6FEZ
Ryegrass mottle virus protease domain
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293 | 0.1 M HEPES 7.5, 22.5% PEG 3350, 0.22M LiSO4, 3% DMSO |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.07 | 59.93 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 37.11 | α = 90 |
b = 115.99 | β = 105.27 |
c = 57.92 | 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 | 90 | PIXEL | DECTRIS PILATUS 6M | 2017-11-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.9184 | BESSY | 14.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 2.3 | 57.99 | 95.98 | 0.123 | 0.149 | 0.083 | 0.989 | 5.3 | 3 | 19160 | 45.496 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.3 | 2.42 | 98.69 | 0.548 | 0.662 | 0.365 | 0.644 | 2.1 | 3.1 |
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 | 1ZYO | 2.3 | 57.99 | 19160 | 1002 | 95.98 | 0.23229 | 0.22946 | 0.29018 | RANDOM | 45.366 |
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] | |
-1.79 | -0.03 | -3.06 | 4.24 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.678 |
r_dihedral_angle_4_deg | 21.571 |
r_dihedral_angle_3_deg | 20.435 |
r_long_range_B_other | 8.737 |
r_long_range_B_refined | 8.735 |
r_dihedral_angle_1_deg | 7.685 |
r_mcangle_it | 5.707 |
r_mcangle_other | 5.706 |
r_scangle_other | 5.241 |
r_angle_other_deg | 3.878 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2779 |
Nucleic Acid Atoms | |
Solvent Atoms | 76 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SCALA | data scaling |
MOLREP | phasing |