6MZZ
Fluoroacetate dehalogenase, room temperature structure, using first 1 degree of total 3 degree oscillation
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6FSX |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | BATCH MODE | 295 | 16-20% PEG 3350, 100mM Tris-Cl pH 8.5, and 200mM CaCl2. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.97 | 37.61 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 41.6 | α = 90 |
b = 79.1 | β = 103 |
c = 83.8 | 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 | 298 | PIXEL | DECTRIS EIGER X 1M | 2018-03-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CHESS BEAMLINE G3 | 1.216 | CHESS | G3 |
Serial Crystallography
Sample delivery method | ||
---|---|---|
Diffraction ID | Description | Sample Delivery Method |
1 | Si fixed target | fixed target |
Measurement | |||||
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Diffraction ID | Pulse Duration | Pulse Repetition Rate | Focal Spot Size | Pulse Energy | Photons Per Pulse |
1 |
Data Reduction | |||
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Diffraction ID | Frames Indexed | Crystal Hits | Total Frames |
1 | 1970 | 1082 | 32000 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.8 | 39.55 | 99.02 | 0.4132 | 0.1648 | 0.954 | 4.71 | 5.7 | 48562 | 34.41 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.8 | 1.864 | 8.37 | 3.646 | 0.0739 |
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 | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 6FSX | 1.8 | 39.55 | 1.33 | 48558 | 2442 | 99.02 | 0.1766 | 0.1749 | 0.2086 | Rnadom | 38.07 |
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 | 16.0784 |
f_angle_d | 0.9526 |
f_chiral_restr | 0.0504 |
f_bond_d | 0.0075 |
f_plane_restr | 0.0063 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4704 |
Nucleic Acid Atoms | |
Solvent Atoms | 217 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |