6YG0

Crystal structure of S287D,T291D MKK7 (MAP2K7), apo form


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.2277.1516% PEG3350, 0.25 M ammonium acetate, 0.1 M tris, pH 8.2
Crystal Properties
Matthews coefficientSolvent content
2.5551.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.37α = 90
b = 69.79β = 90
c = 84.64γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-03-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.97950DiamondI02

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
1236.191000.0660.0710.0270.99713.86.724828
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)
122.111000.9520.9521.030.3870.6930.86.8

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 REPLACEMENTTHROUGHOUT2dyl236.1923559121299.890.19680.19430.2452RANDOM60.822
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]
-0.242.66-2.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.999
r_dihedral_angle_4_deg21.01
r_dihedral_angle_3_deg16.156
r_dihedral_angle_1_deg6.897
r_angle_refined_deg1.442
r_angle_other_deg0.95
r_chiral_restr0.072
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.999
r_dihedral_angle_4_deg21.01
r_dihedral_angle_3_deg16.156
r_dihedral_angle_1_deg6.897
r_angle_refined_deg1.442
r_angle_other_deg0.95
r_chiral_restr0.072
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2229
Nucleic Acid Atoms
Solvent Atoms89
Heterogen Atoms

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing