2CLQ

Structure of mitogen-activated protein kinase kinase kinase 5


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelOtherHOMOLOGY MODEL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
125% PEG3350 0.17M, (NH4)2SO4 15% GLYCEROL
Crystal Properties
Matthews coefficientSolvent content
2.856.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.606α = 90
b = 78.606β = 90
c = 423.279γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2005-10-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

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
12.34799.30.117.714.935817
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)
12.32.3993.90.591.93.4

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 REPLACEMENTTHROUGHOUTHOMOLOGY MODEL2.35033893177899.30.2040.2010.257RANDOM31.17
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]
0.40.20.4-0.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.336
r_dihedral_angle_4_deg23.144
r_dihedral_angle_3_deg17.836
r_scangle_it8.936
r_scbond_it7.76
r_dihedral_angle_1_deg6.081
r_mcangle_it3.995
r_mcbond_it2.899
r_angle_refined_deg1.526
r_angle_other_deg1.017
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.336
r_dihedral_angle_4_deg23.144
r_dihedral_angle_3_deg17.836
r_scangle_it8.936
r_scbond_it7.76
r_dihedral_angle_1_deg6.081
r_mcangle_it3.995
r_mcbond_it2.899
r_angle_refined_deg1.526
r_angle_other_deg1.017
r_symmetry_vdw_other0.232
r_nbd_refined0.215
r_nbd_other0.191
r_nbtor_refined0.179
r_xyhbond_nbd_refined0.168
r_symmetry_vdw_refined0.166
r_symmetry_hbond_refined0.149
r_nbtor_other0.092
r_chiral_restr0.088
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_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 Atoms3989
Nucleic Acid Atoms
Solvent Atoms149
Heterogen Atoms70

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing