Room temperature structure of Glycine max phyA in Pr
Serial Crystallography (SX)
Starting Model(s)
Initial Refinement Model(s) |
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Type | Source | Accession Code | Details |
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experimental model | PDB | 6TC7 | |
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | BATCH MODE | 8.5 | 295 | PEG20K 9%, PEG500MME 18%, 0.1 M Tris-Bicine pH 8.5 |
Crystal Properties |
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Matthews coefficient | Solvent content |
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2.83 | 56.51 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 56.45 | α = 90 |
b = 115.05 | β = 92.68 |
c = 69.8 | γ = 90 |
Symmetry |
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Space Group | P 1 21 1 |
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Diffraction
Diffraction Experiment |
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
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1 | 1 | x-ray | 293 | PIXEL | AGIPD | | 2023-08-24 | M | SINGLE WAVELENGTH |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | FREE ELECTRON LASER | EUROPEAN XFEL BEAMLINE SPB/SFX | 1.33 | European XFEL | SPB/SFX |
Serial Crystallography
Sample delivery method |
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Diffraction ID | Description | Sample Delivery Method |
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1 | | injection |
Injection |
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Diffraction ID | Description | Flow Rate | Injector Diameter | Injection Power | Injector Nozzle | Filter Size | Carrier Solvent |
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1 | GVDN | undefined (µl/min) | undefined (µm) | | | | |
Data Collection
Overall |
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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 |
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1 | 2.2 | 20.49 | 100 | 0.9775 | 0.1716 | 5.58 | 491.6 | | 45132 | | | 39.49 |
Highest Resolution Shell |
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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) |
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1 | 2.2 | 2.28 | 100 | | 0.5286 | 0.9743 | 0.96 | 371.1 | |
Refinement
Statistics |
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B |
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X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2.2 | 20.48 | 1.34 | 45021 | 2306 | 99.8 | 0.2058 | 0.2038 | 0.2037 | 0.241 | 0.2397 | 47.88 |
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] |
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| | | | | |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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f_dihedral_angle_d | 18.3145 |
f_angle_d | 1.4645 |
f_chiral_restr | 0.0803 |
f_plane_restr | 0.0149 |
f_bond_d | 0.01 |
Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 4803 |
Nucleic Acid Atoms | |
Solvent Atoms | 138 |
Heterogen Atoms | 86 |
Software
Software |
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Software Name | Purpose |
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PHENIX | refinement |
CrystFEL | data reduction |
CrystFEL | data scaling |
PHASER | phasing |