6CPZ
Selenomethionine mutant (I6Sem) of protein GB1 examined by X-ray diffraction
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2QMT |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.7 | 283.15 | 48% MPD 20% IPA 25 mM sodium acetate buffer pH 4.7 20 mg/ml protein in 25 mM sodium acetate buffer pH 5.5 and 2 mM TCEP |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.99 | 38.32 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 27.89 | α = 90 |
b = 36.489 | β = 98.67 |
c = 48.94 | 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 PILATUS3 6M | 2017-08-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.1 | 0.9795 | ALS | 5.0.1 |
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 | 1.12 | 27.571 | 97.43 | 0.01784 | 0.02524 | 0.01784 | 0.999 | 12.98 | 2 | 69779 | 7.95 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.12 | 1.16 |
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 | 2QMT | 1.12 | 27.571 | 1.36 | 69779 | 3802 | 95.06 | 0.1379 | 0.1369 | 0.1561 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 20.938 |
f_angle_d | 1.081 |
f_chiral_restr | 0.086 |
f_bond_d | 0.008 |
f_plane_restr | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 868 |
Nucleic Acid Atoms | |
Solvent Atoms | 179 |
Heterogen Atoms | 52 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
PHENIX | model building |
PHASER | phasing |
XDS | data scaling |