7OB7
CPR-C4 - novel protease from the Candidate Phyla Radiation (CPR)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | sodium malonate dibasic monohydrate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.61 | 52.8 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 56.307 | α = 90 |
b = 79.731 | β = 90 |
c = 126.196 | γ = 90 |
Symmetry | |
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Space Group | I 2 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 | PIXEL | DECTRIS PILATUS3 6M | 2019-12-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 1.2819 | Diamond | I24 |
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 | 2.581 | 67.405 | 98.9 | 0.505 | 0.562 | 0.243 | 0.968 | 6.8 | 9.7 | 9190 |
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 | 2.581 | 2.69 | 7.895 | 8.889 | 3.982 | 0.181 | 8.2 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 7OB6 | 2.682 | 67.405 | 8193 | 398 | 98.747 | 0.236 | 0.2348 | 0.2506 | 49.032 |
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] | |
-1.94 | 6.08 | -4.14 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.876 |
r_dihedral_angle_4_deg | 19.829 |
r_lrange_it | 14.438 |
r_dihedral_angle_3_deg | 14.335 |
r_scangle_it | 8.816 |
r_dihedral_angle_1_deg | 7.331 |
r_mcangle_it | 5.989 |
r_scbond_it | 5.74 |
r_mcbond_it | 3.833 |
r_angle_refined_deg | 1.406 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1653 |
Nucleic Acid Atoms | |
Solvent Atoms | 18 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
REFMAC | refinement |
Aimless | data scaling |
DIALS | data reduction |
pointless | data scaling |
PHASER | phasing |