5MAG

Crystal structure of MELK in complex with an inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherin house MELK structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529310-20% PEG 3350 or PEG 4000, 0.1 M BIS TRIS pH 6.5, 0.6M NaCl
Crystal Properties
Matthews coefficientSolvent content
2.2645.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.18α = 90
b = 62.81β = 90
c = 94.11γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-FToroidal mirror2016-10-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.976254ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.3594.1195.90.1310.9817.74.615037
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.352.4899.90.3690.8853.94.8

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 REPLACEMENTTHROUGHOUTin house MELK structure2.3552.241430369495.720.196160.193510.25242RANDOM36.056
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]
-3.3-0.093.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.189
r_dihedral_angle_4_deg23.329
r_dihedral_angle_3_deg15.865
r_dihedral_angle_1_deg6.259
r_long_range_B_refined5.768
r_long_range_B_other5.767
r_scangle_other3.788
r_angle_other_deg3.576
r_mcangle_it3.22
r_mcangle_other3.219
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.189
r_dihedral_angle_4_deg23.329
r_dihedral_angle_3_deg15.865
r_dihedral_angle_1_deg6.259
r_long_range_B_refined5.768
r_long_range_B_other5.767
r_scangle_other3.788
r_angle_other_deg3.576
r_mcangle_it3.22
r_mcangle_other3.219
r_scbond_it2.265
r_scbond_other2.264
r_mcbond_other1.924
r_mcbond_it1.923
r_angle_refined_deg1.405
r_chiral_restr0.079
r_bond_refined_d0.009
r_gen_planes_other0.006
r_gen_planes_refined0.004
r_bond_other_d
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 Atoms2565
Nucleic Acid Atoms
Solvent Atoms82
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing