5BYZ

ERK5 in complex with small molecule


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP27711 % PEG4000 0.01 M MgCl2 0.18 M Na-Formiate 0.10 M MES, pH=6.50 0.01 M Tris/Cl, pH=8.50
Crystal Properties
Matthews coefficientSolvent content
3.2462.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.401α = 90
b = 93.401β = 90
c = 116.28γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-05-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.00003SLSX06SA

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
11.6572.8299.50.04324.227.162385
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)
11.651.7498.80.0697

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 REPLACEMENTTHROUGHOUT1.6572.8258548350699.470.17470.173670.19225RANDOM17.515
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]
0.880.88-1.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.542
r_dihedral_angle_4_deg17.934
r_dihedral_angle_3_deg12.014
r_dihedral_angle_1_deg5.289
r_scangle_it4.359
r_scbond_it2.854
r_mcangle_it1.98
r_angle_refined_deg1.203
r_mcbond_it1.203
r_angle_other_deg0.994
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.542
r_dihedral_angle_4_deg17.934
r_dihedral_angle_3_deg12.014
r_dihedral_angle_1_deg5.289
r_scangle_it4.359
r_scbond_it2.854
r_mcangle_it1.98
r_angle_refined_deg1.203
r_mcbond_it1.203
r_angle_other_deg0.994
r_mcbond_other0.358
r_chiral_restr0.067
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2804
Nucleic Acid Atoms
Solvent Atoms336
Heterogen Atoms70

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
MOLREPphasing