8PQN
NQO1 bound to RBS-10
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1D4A |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 9.2 | 293 | 300mM TRIS 9.2 2.8M Ammonium Sulfate |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.77 | 55.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 70.748 | α = 90 |
b = 178.369 | β = 90 |
c = 210.479 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | Kirkpatrick-Baez | 2023-04-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALBA BEAMLINE XALOC | 0.97918 | ALBA | XALOC |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 3.8 | 89.18 | 100 | 0.079 | 11.4 | 6.1 | 13579 | 121.5 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 3.8 | 4.01 | 100 | 0.495 | 4.1 | 6.2 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Work | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 3.8 | 68.132 | 13543 | 687 | 99.904 | 0.266 | 0.261 | 0.3616 | 209.703 |
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] | |
31.519 | -11.45 | -20.069 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_lrange_it | 24.007 |
r_lrange_other | 24.006 |
r_mcangle_it | 17.181 |
r_mcangle_other | 17.18 |
r_scangle_it | 14.056 |
r_scangle_other | 14.055 |
r_dihedral_angle_3_deg | 14.012 |
r_dihedral_angle_6_deg | 11.011 |
r_mcbond_it | 10.391 |
r_mcbond_other | 10.39 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 8696 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 160 |
Software
Software | |
---|---|
Software Name | Purpose |
MxCuBE | data collection |
iMOSFLM | data reduction |
pointless | data scaling |
SCALA | data scaling |
PHASER | phasing |
REFMAC | refinement |
Coot | model building |