5SA4
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z239136710
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5 | 293 | 0.1 M Na3 Citrate pH 5,14% w/v PEG6000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.62 | 73.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 150.155 | α = 90 |
b = 150.155 | β = 90 |
c = 111.134 | γ = 120 |
Symmetry | |
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Space Group | P 63 |
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 | PIXEL | DECTRIS PILATUS 6M | 2020-07-07 | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.91256 | Diamond | I04-1 |
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 | 2.05 | 130.07 | 99.6 | 0.197 | 0.208 | 0.066 | 0.995 | 6.4 | 9.8 | 89441 | 43.62 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.05 | 2.08 | 92.1 | 2.868 | 3.021 | 0.946 | 0.459 | 10.2 | 4252 |
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 | FOURIER SYNTHESIS | THROUGHOUT | 6X1B | 2.046 | 130.04 | 89218 | 4436 | 99.5 | 0.2051 | 0.204 | 0.2252 | RANDOM | 50.55 |
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] | |
4.9323 | 4.9323 | -9.8647 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 16.88 |
t_omega_torsion | 3.61 |
t_angle_deg | 1.04 |
t_bond_d | 0.008 |
t_dihedral_angle_d | |
t_trig_c_planes | |
t_gen_planes | |
t_it | |
t_nbd | |
t_improper_torsion |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5500 |
Nucleic Acid Atoms | |
Solvent Atoms | 619 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
BUSTER | refinement |
Aimless | data scaling |
PDB_EXTRACT | data extraction |
XDS | data reduction |
REFMAC | phasing |