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Crystal structure of MELK in complex with an inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other in house MELK structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 10-20% PEG 3350 or PEG 4000, 0.1M BIS TRIS pH 6.5, 0.6 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.35 47.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.282 α = 90 b = 91.206 β = 90 c = 59.649 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F Toroidal mirror 2016-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.976254 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.9 49.93 94.7 0.032 1 21.3 4.5 22643 2
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) Redundancy Number Unique Reflections (All) 1 1.9 2 84.2 0.224 0.974 5.6 4.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT in house MELK structure 1.9 49.93 19461 1012 73.42 0.18672 0.18525 0.21366 0.2178 RANDOM 43.972
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] 0.25 3.14 -3.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.184 r_dihedral_angle_4_deg 16.815 r_dihedral_angle_3_deg 14.088 r_long_range_B_other 7.283 r_long_range_B_refined 7.281 r_dihedral_angle_1_deg 5.953 r_scangle_other 5.425 r_mcangle_it 4.33 r_mcangle_other 4.33 r_angle_other_deg 3.565
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.184 r_dihedral_angle_4_deg 16.815 r_dihedral_angle_3_deg 14.088 r_long_range_B_other 7.283 r_long_range_B_refined 7.281 r_dihedral_angle_1_deg 5.953 r_scangle_other 5.425 r_mcangle_it 4.33 r_mcangle_other 4.33 r_angle_other_deg 3.565 r_scbond_it 3.419 r_scbond_other 3.418 r_mcbond_it 2.92 r_mcbond_other 2.917 r_angle_refined_deg 1.855 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_other 0.01 r_gen_planes_refined 0.007 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 Atoms Number Protein Atoms 2572 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing