7V0G
Structure of cAMP-dependent protein kinase using a MD-MX procedure, produced using 1.63 Angstrom data
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 3FJQ |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | 20% PEG 4000, 0.05 M MES pH 5.2, 0.05 M MgCl2, and 0.005 M DTT |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.72 | 54.75 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 58.976 | α = 90 |
b = 79.744 | β = 90 |
c = 99.058 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 285 | PIXEL | DECTRIS PILATUS3 S 6M | Primary Mirror: Flat; Secondary Mirror: uncooled cyllindrical silicon bent into torroid; 2:1 demagnification; Both mirrors coated with Pt/Rh | 2018-12-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | 1.11583 | ALS | 8.3.1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.63 | 47.42 | 99.47 | 0.1056 | 0.1188 | 0.0534 | 0.996 | 7.39 | 4.6 | 58663 | 19.77 |
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 | 1.63 | 1.688 | 99.79 | 1.374 | 0.1188 | 0.6996 | 0.529 | 1.27 | 4.6 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 3FJQ | 1.63 | 42.07 | 1.33 | 58640 | 1999 | 99.44 | 0.1179 | 0.1163 | 0.1625 | 30.32 |
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 | 19.1894 |
f_angle_d | 0.994 |
f_chiral_restr | 0.0549 |
f_plane_restr | 0.0108 |
f_bond_d | 0.0083 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2858 |
Nucleic Acid Atoms | |
Solvent Atoms | 495 |
Heterogen Atoms | 39 |
Software
Software | |
---|---|
Software Name | Purpose |
PHENIX | refinement |
PHASER | phasing |
DIALS | data reduction |
xia2 | data reduction |
Aimless | data scaling |