5MAI

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
2.5150.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 169.134α = 90
b = 169.134β = 90
c = 169.134γ = 90
Symmetry
Space GroupI 41 3 2

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
12.1553.481000.0630.99918.18.622725
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)
12.152.271000.7930.7983.18.5

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 structure2.1553.4821616108999.890.191620.189390.2371RANDOM53.954
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.164
r_dihedral_angle_4_deg19.596
r_dihedral_angle_3_deg17.017
r_long_range_B_refined8.957
r_long_range_B_other8.956
r_scangle_other7.037
r_dihedral_angle_1_deg6.016
r_mcangle_it5.189
r_mcangle_other5.188
r_scbond_it4.487
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.164
r_dihedral_angle_4_deg19.596
r_dihedral_angle_3_deg17.017
r_long_range_B_refined8.957
r_long_range_B_other8.956
r_scangle_other7.037
r_dihedral_angle_1_deg6.016
r_mcangle_it5.189
r_mcangle_other5.188
r_scbond_it4.487
r_scbond_other4.485
r_mcbond_it3.605
r_mcbond_other3.603
r_angle_refined_deg1.562
r_angle_other_deg1.008
r_chiral_restr0.087
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms2555
Nucleic Acid Atoms
Solvent Atoms65
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing