5M5A

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, 0.1M BIS TRIS pH 6.5, 0.6 M NaCl
Crystal Properties
Matthews coefficientSolvent content
2.3547.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.282α = 90
b = 91.206β = 90
c = 59.649γ = 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
11.949.9394.70.032121.34.5226432
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)
11.9284.20.2240.9745.64.6

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 structure1.949.9319461101273.420.186720.185250.21366RANDOM43.972
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]
0.253.14-3.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.184
r_dihedral_angle_4_deg16.815
r_dihedral_angle_3_deg14.088
r_long_range_B_other7.283
r_long_range_B_refined7.281
r_dihedral_angle_1_deg5.953
r_scangle_other5.425
r_mcangle_it4.33
r_mcangle_other4.33
r_angle_other_deg3.565
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.184
r_dihedral_angle_4_deg16.815
r_dihedral_angle_3_deg14.088
r_long_range_B_other7.283
r_long_range_B_refined7.281
r_dihedral_angle_1_deg5.953
r_scangle_other5.425
r_mcangle_it4.33
r_mcangle_other4.33
r_angle_other_deg3.565
r_scbond_it3.419
r_scbond_other3.418
r_mcbond_it2.92
r_mcbond_other2.917
r_angle_refined_deg1.855
r_chiral_restr0.081
r_bond_refined_d0.012
r_gen_planes_other0.01
r_gen_planes_refined0.007
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 Atoms2572
Nucleic Acid Atoms
Solvent Atoms106
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing