8EKO
Sperm whale myoglobin mutant L29H F33W F43H (F33W CuBMb)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 277 | F33W CuBMb (1.0 mM) in 100 mM tris pH 8, (pH adjusted H2SO4), was mixed 1:3 with well buffer (0.1 M sodium cacodylate pH 6.5, 0.2 M sodium acetate trihydrate with 30% w/v polyethylene glycol 8000) using the hanging drop method with 300 uL well buffer in the well of the crystallization tray. Crystals obtained by this method were soaked with 10 eq CuSO4 in a mixture of F33W CuBMb and well buffer consistent with the original drop conditions to avoid dissolving the crystals and subsequently with 15eq potassium cyanide, in a mixture of E-F33W-CuBMb and well buffer using pH 7.0 sodium cacodylate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.16 | 43.07 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 40.059 | α = 90 |
b = 48.07 | β = 90 |
c = 77.739 | γ = 90 |
Symmetry | |
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Space Group | P 21 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 | DECTRIS PILATUS3 6M | 2019-06-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.2 | 1.0 | ALS | 5.0.2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim 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 | 1.34 | 35.61 | 99.91 | 0.1921 | 0.02717 | 0.999 | 19.35 | 2 | 34356 | 9.35 |
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) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.34 | 1.39 | 99.71 | 0.05665 | 0.08011 | 0.987 | 2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 4FWY | 1.34 | 35.61 | 1.35 | 34355 | 1705 | 99.92 | 0.1406 | 0.1394 | 0.1642 | 15.53 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 13.8673 |
f_angle_d | 0.9589 |
f_chiral_restr | 0.0883 |
f_plane_restr | 0.0082 |
f_bond_d | 0.0059 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1217 |
Nucleic Acid Atoms | |
Solvent Atoms | 139 |
Heterogen Atoms | 43 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHENIX | phasing |