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Structure of crolibulin in complex with tubulin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4I55
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 6% POLYETHYLENE GLYCOL 4000, 8% GLYCEROL, 0.1 M MES, 30 MM CACL2, 30 MM MGCL2, PH 6.7
Crystal Properties Matthews coefficient Solvent content 2.92 57.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.544 α = 90 b = 157.329 β = 90 c = 184.031 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 PILATUS3 S 6M 2018-01-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9798 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.5 50 99.9 0.086 20.6 6.8 108297
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.54 100 0.8 2.3 7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4I55 2.5 48.42 101772 5334 97.79 0.24283 0.24078 0.2422 0.28185 0.2807 RANDOM 45.181
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] 0.16 -0.17 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.79 r_dihedral_angle_3_deg 16.489 r_dihedral_angle_4_deg 14.464 r_long_range_B_refined 7.976 r_long_range_B_other 7.975 r_dihedral_angle_1_deg 7.353 r_mcangle_it 5.189 r_mcangle_other 5.189 r_scangle_other 4.868 r_mcbond_it 3.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.79 r_dihedral_angle_3_deg 16.489 r_dihedral_angle_4_deg 14.464 r_long_range_B_refined 7.976 r_long_range_B_other 7.975 r_dihedral_angle_1_deg 7.353 r_mcangle_it 5.189 r_mcangle_other 5.189 r_scangle_other 4.868 r_mcbond_it 3.136 r_mcbond_other 3.131 r_scbond_it 2.884 r_scbond_other 2.884 r_angle_refined_deg 1.441 r_angle_other_deg 1.172 r_chiral_restr 0.06 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 17019 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 212
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing