6NXA
ECAII(D90T,K162T) MUTANT AT PH 7
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 293 | Protein, at the concentration 15 mg/ml in 50 mM HEPES buffer pH 7 and 150 mM sodium chloride was mixed with equivolume solution of precipitant that contained, 17% (w/v) PEG3350 and 0.17 M ammonium citrate pH 7. Resulting droplets were equilibrated against the precipitant. For the data collection, crystal was briefly transferred to cryo-protecting solution, which had the same composition as precipitant, except concentration of PEG3350 was increased to 35 % (v/w/) and 10% (v/v), and also contained 15% of glycerol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.11 | 41.61 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 151.885 | α = 90 |
b = 62.509 | β = 118.19 |
c = 143.16 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 EIGER R 4M | Multilayer X-ray mirrors VariMax HF | 2018-07-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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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 Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.93 | 40 | 96.1 | 0.1 | 0.119 | 0.064 | 7.8 | 3.3 | 86035 |
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 | 1.93 | 1.96 | 79 | 0.512 | 0.628 | 0.359 | 0.646 | 2.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.93 | 26.54 | 83055 | 2649 | 95.95 | 0.1547 | 0.1524 | 0.2274 | RANDOM | 33.522 |
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] | |
0.09 | 0.04 | -0.4 | 0.17 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.891 |
r_dihedral_angle_4_deg | 18.538 |
r_dihedral_angle_3_deg | 15.285 |
r_dihedral_angle_1_deg | 7.386 |
r_angle_refined_deg | 2.317 |
r_angle_other_deg | 1.569 |
r_chiral_restr | 0.11 |
r_bond_refined_d | 0.02 |
r_gen_planes_refined | 0.015 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9410 |
Nucleic Acid Atoms | |
Solvent Atoms | 1184 |
Heterogen Atoms | 34 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
REFMAC | phasing |