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The structure of SB-1-202-tubulin complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EZY
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 2.9 57.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.541 α = 90 b = 158.033 β = 90 c = 181.87 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 2018-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97937 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 2.45 50 100 0.148 28.5 12.9 111555
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 2.45 2.49 1.2 2
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 5ezy 2.45 50 103706 5580 97.53 0.19761 0.19554 0.1996 0.23628 0.2379 RANDOM 46.422
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] 0.58 -0.17 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.126 r_dihedral_angle_4_deg 14.378 r_dihedral_angle_3_deg 12.855 r_long_range_B_refined 6.964 r_long_range_B_other 6.921 r_dihedral_angle_1_deg 6.285 r_scangle_other 4.237 r_mcangle_it 3.879 r_mcangle_other 3.879 r_scbond_it 2.493
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.126 r_dihedral_angle_4_deg 14.378 r_dihedral_angle_3_deg 12.855 r_long_range_B_refined 6.964 r_long_range_B_other 6.921 r_dihedral_angle_1_deg 6.285 r_scangle_other 4.237 r_mcangle_it 3.879 r_mcangle_other 3.879 r_scbond_it 2.493 r_scbond_other 2.493 r_mcbond_it 2.312 r_mcbond_other 2.312 r_angle_refined_deg 1.352 r_angle_other_deg 0.967 r_chiral_restr 0.091 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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 17506 Nucleic Acid Atoms Solvent Atoms 732 Heterogen Atoms 250
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing