6OPK

Phosphorylated ERK2 with Vertex-11e


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ERK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529316.5% PEG3350,100 mM Tris-HCl pH 8.5
Crystal Properties
Matthews coefficientSolvent content
3.0559.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.986α = 90
b = 78.139β = 90
c = 152.601γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2015-06-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.0332APS23-ID-D

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
12.47301000.0989.56.119482
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.472.5499.90.931.0540.494.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT2ERK2.54301637289699.90.195620.193030.24081RANDOM73.051
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]
-0.020.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.813
r_dihedral_angle_4_deg21.327
r_dihedral_angle_3_deg16.743
r_long_range_B_other11.264
r_long_range_B_refined11.217
r_scangle_other9.13
r_mcangle_it8.33
r_mcangle_other8.329
r_dihedral_angle_1_deg7.163
r_scbond_other6.595
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.813
r_dihedral_angle_4_deg21.327
r_dihedral_angle_3_deg16.743
r_long_range_B_other11.264
r_long_range_B_refined11.217
r_scangle_other9.13
r_mcangle_it8.33
r_mcangle_other8.329
r_dihedral_angle_1_deg7.163
r_scbond_other6.595
r_scbond_it6.577
r_mcbond_it6.005
r_mcbond_other5.997
r_angle_refined_deg1.657
r_angle_other_deg1.187
r_chiral_restr0.064
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2839
Nucleic Acid Atoms
Solvent Atoms20
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing