6OPI

phosphorylated ERK2 with SCH-CPD336


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.229320% (w/v) PEG3350, 100 mM Na cacodylate pH 7.2, 600 mM NaCl, 10 mM MnCl2
Crystal Properties
Matthews coefficientSolvent content
2.4750.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.394α = 90
b = 77.64β = 90
c = 126.536γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++Osmic confocal2008-08-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E1.5418

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
133099.80.0987.84.68550
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)
133.161000.3430.3870.1772.24.7

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 REPLACEMENTTHROUGHOUT2ERK322.06822641099.670.188520.184890.26046RANDOM46.605
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]
20.1-2.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.73
r_dihedral_angle_4_deg25.127
r_dihedral_angle_3_deg18.279
r_long_range_B_other8.045
r_long_range_B_refined8.002
r_dihedral_angle_1_deg7.395
r_scangle_other5.829
r_mcangle_it5.7
r_mcangle_other5.699
r_mcbond_it3.706
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.73
r_dihedral_angle_4_deg25.127
r_dihedral_angle_3_deg18.279
r_long_range_B_other8.045
r_long_range_B_refined8.002
r_dihedral_angle_1_deg7.395
r_scangle_other5.829
r_mcangle_it5.7
r_mcangle_other5.699
r_mcbond_it3.706
r_mcbond_other3.698
r_scbond_other3.696
r_scbond_it3.678
r_angle_refined_deg1.741
r_angle_other_deg1.187
r_chiral_restr0.061
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms2662
Nucleic Acid Atoms
Solvent Atoms30
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing