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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, 0.1 M BIS TRIS pH 6.5, 0.6M NaCl
Crystal Properties Matthews coefficient Solvent content 2.51 50.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.134 α = 90 b = 169.134 β = 90 c = 169.134 γ = 90
Symmetry Space Group I 41 3 2
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 2.15 53.48 100 0.063 0.999 18.1 8.6 22725
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 2.15 2.27 100 0.793 0.798 3.1 8.5
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 2.15 53.48 21616 1089 99.89 0.19162 0.18939 0.2371 0.2336 RANDOM 53.954
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.164 r_dihedral_angle_4_deg 19.596 r_dihedral_angle_3_deg 17.017 r_long_range_B_refined 8.957 r_long_range_B_other 8.956 r_scangle_other 7.037 r_dihedral_angle_1_deg 6.016 r_mcangle_it 5.189 r_mcangle_other 5.188 r_scbond_it 4.487
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.164 r_dihedral_angle_4_deg 19.596 r_dihedral_angle_3_deg 17.017 r_long_range_B_refined 8.957 r_long_range_B_other 8.956 r_scangle_other 7.037 r_dihedral_angle_1_deg 6.016 r_mcangle_it 5.189 r_mcangle_other 5.188 r_scbond_it 4.487 r_scbond_other 4.485 r_mcbond_it 3.605 r_mcbond_other 3.603 r_angle_refined_deg 1.562 r_angle_other_deg 1.008 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 Atoms Number Protein Atoms 2555 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing