5HOL
The crystal structure of the MERS-CoV macro domain with ADP-ribose
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2FAV |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 291 | 0.1 M Bis-Tris propane pH 7.0, 1.3 M sodium citrate tribasic dihydrate. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.64 | 53.39 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 31.3 | ¦Á = 90 |
b = 66.53 | ¦Â = 90 |
c = 89.5 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 2 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | PSI PILATUS 6M | 2013-05-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, DESY BEAMLINE P11 | 0.992 | PETRA III, DESY | P11 |
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 | 1.59 | 53.39 | 100 | 0.047 | 27.6 | 10.9 | 24489 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.59 | 1.68 | 100 | 0.211 | 9.2 | 10.8 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | FREE R-VALUE | 2FAV | 1.59 | 53.39 | 24489 | 1315 | 99.99 | 0.14219 | 0.14092 | 0.16534 | RANDOM | 20.767 |
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] | |
-1.19 | 1.19 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.781 |
r_dihedral_angle_4_deg | 18.385 |
r_dihedral_angle_3_deg | 12.511 |
r_long_range_B_refined | 7.982 |
r_long_range_B_other | 7.607 |
r_dihedral_angle_1_deg | 6.693 |
r_scangle_other | 5.194 |
r_scbond_it | 3.701 |
r_scbond_other | 3.698 |
r_mcangle_other | 3.346 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1242 |
Nucleic Acid Atoms | |
Solvent Atoms | 179 |
Heterogen Atoms | 36 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
MOLREP | phasing |