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Tubulin-podophyllotoxin: stathmin-like domain complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SA0 PDB ENTRY 1SA0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 PEG, PIPES BUFFER, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.88 68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 328.061 α = 90 b = 328.061 β = 90 c = 54.301 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC 2000-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.933 ESRF ID14-1
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 4.2 30 98.3 0.06 18 3.26 24624
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) 4.2 4.3 90.2 0.482 2 2.3
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1SA0 4.2 20 23198 1230 98.32 0.20643 0.20643 0.20369 0.25935 RANDOM 116.49
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] -1.57 -0.78 -1.57 2.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 9.523 r_angle_refined_deg 2.091 r_symmetry_vdw_refined 0.348 r_nbd_refined 0.323 r_xyhbond_nbd_refined 0.239 r_scangle_it 0.231 r_metal_ion_refined 0.219 r_symmetry_hbond_refined 0.212 r_scbond_it 0.156 r_chiral_restr 0.154
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 9.523 r_angle_refined_deg 2.091 r_symmetry_vdw_refined 0.348 r_nbd_refined 0.323 r_xyhbond_nbd_refined 0.239 r_scangle_it 0.231 r_metal_ion_refined 0.219 r_symmetry_hbond_refined 0.212 r_scbond_it 0.156 r_chiral_restr 0.154 r_mcangle_it 0.12 r_mcbond_it 0.069 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13998 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 182
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement