6YG4

Crystal structure of MKK7 (MAP2K7) in complex with K00007


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.2277.1519% PEG3350, 0.1 M ammonium acetate, 0.1 M tris, pH 8.2
Crystal Properties
Matthews coefficientSolvent content
2.3347.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.1α = 90
b = 72.63β = 90
c = 83.079γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2014-08-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97949DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.336.0699.60.0660.0750.0340.99811.24.615049
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.4299.80.7450.7450.8350.3710.69114.7

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 REPLACEMENTTHROUGHOUT2dyl2.336.061426374999.390.21290.21060.2549RANDOM65.022
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]
1.22-5.163.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.042
r_dihedral_angle_4_deg19.601
r_dihedral_angle_3_deg15.269
r_dihedral_angle_1_deg7.386
r_angle_refined_deg1.263
r_angle_other_deg1.185
r_chiral_restr0.055
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.042
r_dihedral_angle_4_deg19.601
r_dihedral_angle_3_deg15.269
r_dihedral_angle_1_deg7.386
r_angle_refined_deg1.263
r_angle_other_deg1.185
r_chiral_restr0.055
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2064
Nucleic Acid Atoms
Solvent Atoms34
Heterogen Atoms40

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing