6ZAL
Room temperature XFEL Isopenicillin N synthase structure in complex with Fe and ACV after exposure to dioxygen for 500ms without glycerol.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1BLZ |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | BATCH MODE | 8.5 | 298 | 1.7 M Li2SO4, 0.1 M TRIS pH8.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.15 | 42.85 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 41.922 | α = 90 |
b = 75.529 | β = 90 |
c = 102.137 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 298 | CCD | RAYONIX MX170-HS | 2018-05-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | FREE ELECTRON LASER | SLAC LCLS BEAMLINE MFX | 1.31145 | SLAC LCLS | MFX |
Serial Crystallography
Sample delivery method | ||
---|---|---|
Diffraction ID | Description | Sample Delivery Method |
1 | injection |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | CC (Half) | R Split (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 | 1.83 | 38.782 | 99.98 | 0.959 | 0.171 | 61.274 | 93.13 | 29482 | 26.8165216571 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.83 | 1.862 | 99.09 | 0.264 | 0.843 | 1.67 | 34.65 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | THROUGHOUT | 1BLZ | 1.83 | 38.7819 | 1.3268 | 29316 | 1995 | 99.83313 | 0.1708 | 0.168 | 0.2091 | 34.421 |
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 | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 8.722653 |
f_angle_d | 0.633627 |
f_chiral_restr | 0.047768 |
f_plane_restr | 0.004377 |
f_bond_d | 0.003876 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2578 |
Nucleic Acid Atoms | |
Solvent Atoms | 151 |
Heterogen Atoms | 32 |
Software
Software | |
---|---|
Software Name | Purpose |
PHENIX | refinement |
cctbx.xfel | data reduction |
PHASER | phasing |
cxi.merge | data scaling |