5MAF

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
2.1743.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.913α = 90
b = 63.713β = 90
c = 91.292γ = 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
12.852.2599.80.1290.9939.869059
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)
12.82.9599.80.7330.7742.66.2

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 structure2.852.25855047699.760.212070.209650.25919RANDOM56.237
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]
-3.460.383.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.918
r_dihedral_angle_4_deg14.749
r_dihedral_angle_3_deg14.222
r_dihedral_angle_1_deg5.444
r_long_range_B_refined5.013
r_long_range_B_other5.012
r_mcangle_it3.016
r_mcangle_other3.015
r_scangle_other2.918
r_mcbond_it1.756
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.918
r_dihedral_angle_4_deg14.749
r_dihedral_angle_3_deg14.222
r_dihedral_angle_1_deg5.444
r_long_range_B_refined5.013
r_long_range_B_other5.012
r_mcangle_it3.016
r_mcangle_other3.015
r_scangle_other2.918
r_mcbond_it1.756
r_mcbond_other1.752
r_scbond_it1.661
r_scbond_other1.66
r_angle_refined_deg1.204
r_angle_other_deg1.023
r_chiral_restr0.06
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms2578
Nucleic Acid Atoms
Solvent Atoms29
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing