8QW0
Human NDPK-C in complex with GDP
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 5.4 | 291 | 6% PEG 3350, 150 mM Li2SO4, 100 mM Tri-sodium citrate pH 5.4 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.17 | 43.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 104.34 | α = 90 |
b = 78.64 | β = 97.561 |
c = 112.37 | 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 | 100 | PIXEL | DECTRIS EIGER X 4M | Vertical CRL / horizontal eliptical mirror | 2021-05-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE MASSIF-3 | 0.9677 | ESRF | MASSIF-3 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim 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 | 2.17 | 46.592 | 99.5 | 0.152 | 0.16 | 0.998 | 9.64 | 10.3 | 94493 | 46.2 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.17 | 2.23 | 94.2 | 1.388 | 1.495 | 0.549 | 1.04 | 7.2 |
Refinement
Statistics | |||||||||||||||||||
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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 | 2.175 | 46.592 | 94493 | 1996 | 99.551 | 0.19 | 0.1888 | 0.2289 | 49.233 |
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] | |
-0.758 | -0.311 | 1.982 | -1.103 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 16.227 |
r_dihedral_angle_6_deg | 15.36 |
r_dihedral_angle_2_deg | 12.79 |
r_lrange_other | 9.785 |
r_lrange_it | 9.779 |
r_scangle_it | 8.812 |
r_scangle_other | 8.812 |
r_dihedral_angle_1_deg | 6.454 |
r_scbond_it | 6.089 |
r_scbond_other | 6.088 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 14463 |
Nucleic Acid Atoms | |
Solvent Atoms | 303 |
Heterogen Atoms | 346 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |