6RVO
Multicrystal dataset of thaumatin collected using a multilayer monochromator.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1RQW |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | COUNTER-DIFFUSION | 5.6 | 293 | 0.1 M Sodium citrate pH 5.6 0.75M Na/K Tartrate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.92 | 57.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 58.563 | α = 90 |
b = 58.563 | β = 90 |
c = 151.496 | γ = 90 |
Symmetry | |
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Space Group | P 41 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 293 | PIXEL | DECTRIS EIGER2 X 4M | Multilayer monochromator | 2019-05-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE VMXi | 0.979 | Diamond | VMXi |
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 | 1.97 | 58.56 | 99.98 | 0.409 | 0.414 | 0.062 | 0.992 | 8.5 | 38.7 | 19537 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.97 | 2 | 99.79 | 2.179 | 2.323 | 0.78 | 0.389 | 0.7 | 8.6 |
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 | 1RQW | 1.97 | 54.624 | 1.34 | 19444 | 1941 | 99.87 | 0.1451 | 0.1417 | 0.1762 | Random selection |
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 | 2.974 |
f_angle_d | 0.866 |
f_chiral_restr | 0.053 |
f_bond_d | 0.01 |
f_plane_restr | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1540 |
Nucleic Acid Atoms | |
Solvent Atoms | 143 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
DIALS | data reduction |
DIALS | data scaling |
PHASER | phasing |