8AEP
Reductase domain of the carboxylate reductase of Neurospora crassa
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 289.15 | Crystals were grown by mixing 0.5 microL 0.2 M ammonia sulphate, 0.1 M BisTRIS pH 5.5 and 25 percent PEG 3350 with 0.5 microL 18.00 mg per mL NcCAR R-domain in 50 mM MES buffer pH pH 7.0 containing 10 mM magnesium chloride, 150 mM sodium chloride and 1 mM DTT. Crystals appeared after 6-9 weeks under vapor batch conditions. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.65 | 53.56 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 56.235 | α = 90 |
b = 137.487 | β = 112.333 |
c = 66.513 | 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 | 100 | PIXEL | DECTRIS PILATUS 2M | 2018-10-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-2 | 0.87313 | ESRF | ID23-2 |
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 | 48.651 | 99.7 | 0.191 | 0.257 | 0.171 | 0.98 | 5.8 | 3.8 | 41333 |
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 | 2.38 | 0.704 | 0.949 | 0.631 | 0.636 | 3.9 |
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 | 5MSP | 2.3 | 48.651 | 41299 | 2039 | 99.614 | 0.203 | 0.2002 | 0.2586 | 26.121 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.551 | -1.231 | 0.075 | 0.288 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.216 |
r_dihedral_angle_4_deg | 19.938 |
r_dihedral_angle_3_deg | 12.175 |
r_dihedral_angle_1_deg | 7.018 |
r_lrange_it | 6.997 |
r_lrange_other | 6.862 |
r_scangle_it | 4.608 |
r_scangle_other | 4.603 |
r_mcangle_it | 3.915 |
r_mcangle_other | 3.915 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6206 |
Nucleic Acid Atoms | |
Solvent Atoms | 741 |
Heterogen Atoms | 12 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
REFMAC | refinement |
Aimless | data scaling |
XDS | data reduction |
MOLREP | phasing |
Coot | model building |