4QTA

Structure of human ERK2 in complex with SCH772984 revealing a novel inhibitor-induced binding pocket


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ERKpdb entry 1ERK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5277.1530% PEG4000 and 0.2 M ammonium sulphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Crystal Properties
Matthews coefficientSolvent content
2.0239.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.82α = 90
b = 75.54β = 90
c = 103.59γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6MKirkpatrick Baez bimorph mirror pair2013-12-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97960DiamondI04

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
11.453399.90.0912.57.9604416036611.9
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)
11.451.5399.70.712.67.58701

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1ERK1.4561.0426036657320304699.930.160080.158390.19147RANDOM21.194
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]
-0.690.090.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.044
r_dihedral_angle_4_deg18.069
r_dihedral_angle_3_deg11.93
r_long_range_B_other6.889
r_long_range_B_refined6.887
r_dihedral_angle_1_deg5.318
r_scangle_other2.745
r_scbond_it1.8
r_scbond_other1.8
r_angle_refined_deg1.698
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.044
r_dihedral_angle_4_deg18.069
r_dihedral_angle_3_deg11.93
r_long_range_B_other6.889
r_long_range_B_refined6.887
r_dihedral_angle_1_deg5.318
r_scangle_other2.745
r_scbond_it1.8
r_scbond_other1.8
r_angle_refined_deg1.698
r_mcangle_it1.592
r_mcangle_other1.592
r_mcbond_it0.994
r_mcbond_other0.993
r_angle_other_deg0.853
r_chiral_restr0.108
r_bond_refined_d0.016
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2715
Nucleic Acid Atoms
Solvent Atoms409
Heterogen Atoms86

Software

Software
Software NamePurpose
GDAdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling