5EJX
X-ray Free Electron Laser Structure of Cytochrome C Peroxidase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6 | 277 | 10UL (350-400UM PROTEIN), 22% MPD, 50MM TRIS PHOSHATE BUFFER PH 6.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277.2K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.07 | 60.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 107.47 | α = 90 |
b = 74.99 | β = 90 |
c = 51.25 | 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 | CCD | RAYONIX MX-325 | Data collected over two experiments, in Dec 2013 and June 2014 | 2013-12-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | FREE ELECTRON LASER | SLAC LCLS BEAMLINE XPP | 1.306, 1.313 | SLAC LCLS | XPP |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 1.5 | 19.7 | 97.8 | 3.33 | 9.2 | 65592 | 65592 |
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 | 1.5 | 1.6 | 93.8 | 2 | 5.7 |
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 | 3M23 | 1.5 | 19.69 | 62310 | 3280 | 97.78 | 0.23518 | 0.23384 | 0.26055 | RANDOM | 5.141 |
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] | |
0.01 | -0.02 | 0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.43 |
r_dihedral_angle_4_deg | 22.341 |
r_dihedral_angle_3_deg | 12.69 |
r_dihedral_angle_1_deg | 6.185 |
r_long_range_B_refined | 3.895 |
r_long_range_B_other | 3.276 |
r_angle_refined_deg | 1.841 |
r_scangle_other | 1.74 |
r_scbond_it | 1.16 |
r_scbond_other | 1.158 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2352 |
Nucleic Acid Atoms | |
Solvent Atoms | 293 |
Heterogen Atoms | 48 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
MOLREP | phasing |