4HPU

Crystal structure of the catalytic subunit of cAMP-dependent protein kinase displaying partial phosphoryl transfer of AMP-PNP onto a substrate peptide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8277.1550 mM Bicine, 150 mM Ammonium acetate, 10 mM DTT, ~7-10 mg/mL protein Well solution: 2% MPD in a 1 mL well. 80 uL of methanol was added to the well immediately before sealing. Drop was 8 uL of 1:1 protein:well, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K, pH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.6353.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.69α = 90
b = 79.8β = 90
c = 98.14γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.11.0ALS8.2.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.5561.9199.70.07612.85.766294
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.551.6399.20.4463.25.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.5561.9162785335799.510.172920.171760.19448RANDOM15.146
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]
0.57-0.53-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.373
r_dihedral_angle_4_deg17.404
r_dihedral_angle_3_deg13.293
r_dihedral_angle_1_deg5.394
r_scangle_it3.011
r_scbond_it1.86
r_angle_refined_deg1.329
r_mcangle_it1.253
r_mcbond_it0.666
r_chiral_restr0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.373
r_dihedral_angle_4_deg17.404
r_dihedral_angle_3_deg13.293
r_dihedral_angle_1_deg5.394
r_scangle_it3.011
r_scbond_it1.86
r_angle_refined_deg1.329
r_mcangle_it1.253
r_mcbond_it0.666
r_chiral_restr0.09
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2936
Nucleic Acid Atoms
Solvent Atoms432
Heterogen Atoms70

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling