7UJX

Structure of cAMP-dependent protein kinase using a MD-MX procedure, produced using 2.4 Angstrom data


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3FJQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529320% PEG 4000, 0.05 M MES pH 5.2, 0.05 M MgCl2, and 0.005 M DTT
Crystal Properties
Matthews coefficientSolvent content
2.7254.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.976α = 90
b = 79.744β = 90
c = 99.058γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray285PIXELDECTRIS PILATUS3 S 6MPrimary Mirror: Flat; Secondary Mirror: uncooled cyllindrical silicon bent into torroid; 2:1 demagnification; Both mirrors coated with Pt/Rh2018-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.11583ALS8.3.1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.449.5399.940.18290.19050.052720.99315.9131887621.84
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)RedundancyNumber Unique Reflections (All)
12.42.4861000.70150.72940.19740.95913.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3FJQ2.449.531.3418874188899.940.13310.12820.176529.76
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d20.5542
f_angle_d0.7785
f_chiral_restr0.0439
f_plane_restr0.0076
f_bond_d0.0037
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2929
Nucleic Acid Atoms
Solvent Atoms496
Heterogen Atoms39

Software

Software
Software NamePurpose
PHENIXrefinement
PHASERphasing
DIALSdata reduction
xia2data reduction
Aimlessdata scaling
BLENDdata scaling