4QTB

Structure of human ERK1 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 2ZOQpdb entry 2ZOQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8277.1533% PEG4000, 0.1 M Tris pH 8.0 and 0.2 M lithium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Crystal Properties
Matthews coefficientSolvent content
2.244.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.98α = 90
b = 94.01β = 91.71
c = 65.36γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6MKirkpatrick Baez bimorph mirror pair2013-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.91997DiamondI03

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
11.438.1595.80.0898.84.11404191403859.8
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)
11.41.4893.30.6182.23.919971

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 2ZOQ1.432.742140385133341704495.550.148460.147040.17505RANDOM16.182
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]
-0.86-0.071.25-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.14
r_dihedral_angle_4_deg18.793
r_dihedral_angle_3_deg11.41
r_long_range_B_refined6.252
r_long_range_B_other6.252
r_dihedral_angle_1_deg5.695
r_scangle_other2.78
r_scbond_it1.812
r_scbond_other1.812
r_angle_refined_deg1.631
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.14
r_dihedral_angle_4_deg18.793
r_dihedral_angle_3_deg11.41
r_long_range_B_refined6.252
r_long_range_B_other6.252
r_dihedral_angle_1_deg5.695
r_scangle_other2.78
r_scbond_it1.812
r_scbond_other1.812
r_angle_refined_deg1.631
r_mcangle_it1.555
r_mcangle_other1.555
r_mcbond_it0.987
r_mcbond_other0.973
r_angle_other_deg0.789
r_chiral_restr0.108
r_bond_refined_d0.016
r_gen_planes_refined0.012
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5692
Nucleic Acid Atoms
Solvent Atoms1111
Heterogen Atoms193

Software

Software
Software NamePurpose
GDAdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling