8BQF
Adenylate Kinase L107I MUTANT
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7F7U |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 292 | 7.5% PEG 3,350, 7.5% PEG 4,000, 7.5% PEG 2,000, 7.5% PEG 5,000 monomethyl ether, 0.07M ammonium nitrate, 2.5% ethylene glycol and 0.05M MES pH=7. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.33 | 47.11 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 77.975 | α = 90 |
b = 84.49 | β = 90 |
c = 218.493 | γ = 90 |
Symmetry | |
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Space Group | P 2 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 | PIXEL | RIGAKU HyPix-3000 | 2022-03-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU | 1.3405 |
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 | 2.05 | 21.04 | 99.69 | 0.1043 | 0.1117 | 0.03909 | 0.995 | 20.47 | 8.1 | 93318 |
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 | 2.05 | 2.123 | 100 | 0.4044 | 0.435 | 0.1585 | 0.931 | 4.39 | 7.4 |
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 | 7F7U | 2.05 | 21.04 | 93318 | 4792 | 99.8 | 0.22073 | 0.21882 | 0.25789 | RANDOM | 27.461 |
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] | |
0.1 | 1.35 | -1.45 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 27.006 |
r_dihedral_angle_3_deg | 16.319 |
r_dihedral_angle_4_deg | 14.31 |
r_dihedral_angle_1_deg | 7.044 |
r_long_range_B_other | 5.588 |
r_long_range_B_refined | 5.586 |
r_scangle_other | 4.147 |
r_mcangle_it | 3.511 |
r_mcangle_other | 3.51 |
r_scbond_it | 2.688 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9486 |
Nucleic Acid Atoms | |
Solvent Atoms | 223 |
Heterogen Atoms | 338 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
CrysalisPro | data reduction |
CrysalisPro | data scaling |
PHASER | phasing |