4WMF
Crystal structure of catalytically inactive MERS-CoV 3CL protease (C148A) in spacegroup P212121
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2YNA | 2YNA, chain A |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 290 | 20.3 mg/mL protein, well solution: 0,1M Hepes pH 7.5, 0.2M proline, 10% w/v polyethylene glycol 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.93 | 68.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 94.059 | α = 90 |
b = 120.391 | β = 90 |
c = 138.884 | γ = 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 | 100 | CCD | MARRESEARCH | 2014-05-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.97 | 50 | 96.4 | 0.047 | 40.5 | 7 | 107729 |
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 | 1.97 | 2.02 | 93.1 | 0.775 | 2.2 | 5.1 |
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 | 2YNA, chain A | 1.97 | 50 | 102185 | 5370 | 96.24 | 0.19451 | 0.19285 | 0.22612 | RANDOM | 28.459 |
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] | |
-0.71 | 0.58 | 0.13 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.46 |
r_dihedral_angle_4_deg | 20.633 |
r_dihedral_angle_3_deg | 13.335 |
r_dihedral_angle_1_deg | 6.51 |
r_scangle_it | 4.103 |
r_scbond_it | 2.61 |
r_mcangle_it | 1.794 |
r_angle_refined_deg | 1.539 |
r_mcbond_it | 1.001 |
r_angle_other_deg | 0.922 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6800 |
Nucleic Acid Atoms | |
Solvent Atoms | 758 |
Heterogen Atoms | 106 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |