5MAH

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
2.1542.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.667α = 90
b = 63.704β = 90
c = 90.945γ = 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
1243.5598.30.0680.99915.45.123513
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)
122.1198.60.7350.8242.54.9

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 structure243.5522356113097.570.18530.182840.23715RANDOM38.418
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]
-2.48-0.32.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.102
r_dihedral_angle_4_deg19.051
r_dihedral_angle_3_deg14.887
r_long_range_B_refined6.426
r_long_range_B_other6.426
r_dihedral_angle_1_deg5.739
r_scangle_other4.429
r_angle_other_deg3.566
r_mcangle_it3.392
r_mcangle_other3.392
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.102
r_dihedral_angle_4_deg19.051
r_dihedral_angle_3_deg14.887
r_long_range_B_refined6.426
r_long_range_B_other6.426
r_dihedral_angle_1_deg5.739
r_scangle_other4.429
r_angle_other_deg3.566
r_mcangle_it3.392
r_mcangle_other3.392
r_scbond_it2.788
r_scbond_other2.783
r_mcbond_it2.211
r_mcbond_other2.201
r_angle_refined_deg1.439
r_chiral_restr0.076
r_bond_refined_d0.011
r_gen_planes_other0.008
r_gen_planes_refined0.006
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 Atoms2574
Nucleic Acid Atoms
Solvent Atoms96
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing