8YP4 | pdb_00008yp4

Structure of MAP2K1 complexed with 5Z7-oxozeaenol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5HZE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2778% Tacsimete pH 5.0, 19.5% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.4449.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.364α = 90
b = 128.947β = 94.86
c = 65.689γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2023-06-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9SPring-8BL44XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
12.3547.19499.60.99710.15432615
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.352.490.573

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.3545.9330955162999.590.210230.206310.21520.284030.2986RANDOM94.273
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]
-3.471.77-3.696.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.884
r_long_range_B_other15.478
r_long_range_B_refined15.467
r_mcangle_it10.652
r_mcangle_other10.65
r_scangle_other10.192
r_dihedral_angle_2_deg7.871
r_mcbond_it6.903
r_mcbond_other6.902
r_dihedral_angle_1_deg6.492
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.884
r_long_range_B_other15.478
r_long_range_B_refined15.467
r_mcangle_it10.652
r_mcangle_other10.65
r_scangle_other10.192
r_dihedral_angle_2_deg7.871
r_mcbond_it6.903
r_mcbond_other6.902
r_dihedral_angle_1_deg6.492
r_scbond_it6.339
r_scbond_other6.338
r_angle_refined_deg1.426
r_angle_other_deg0.548
r_chiral_restr0.21
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 Atoms4832
Nucleic Acid Atoms
Solvent Atoms137
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing