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Crystal Structures of (S)-(-)-Blebbistatin Analogs bound to Dictyostelium discoideum myosin II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YV3 PDB entry 1YV3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 278 mixing 5 ul of protein with an equal volume of well solution containing
100 mM MOPS, 250 mM MgCl2, 12% PEG 8000, 1 mM TCEP, and 2 mM Thymol, pH 7.0, vapor diffusion, hanging drop, temperature 278K
Crystal Properties Matthews coefficient Solvent content 2.88 57.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.682 α = 90 b = 146.317 β = 90 c = 154.061 γ = 90
Symmetry Space Group C 2 2 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 CCD MAR CCD 165 mm M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 32-ID 1.0 APS 32-ID
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 2.1 50 98.4 0.067 10.1 5.6 57739
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) 2.1 2.18 98.8 0.272 5.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1YV3 2.1 50 54815 2919 98.36 0.19292 0.19059 0.1925 0.23773 0.2425 RANDOM 28.502
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] 1.08 -0.27 -0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.508 r_dihedral_angle_4_deg 16.326 r_dihedral_angle_3_deg 13.862 r_dihedral_angle_1_deg 6.013 r_scangle_it 3.778 r_scbond_it 2.652 r_mcangle_it 1.73 r_angle_refined_deg 1.605 r_mcbond_it 1.1 r_symmetry_vdw_refined 0.327
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.508 r_dihedral_angle_4_deg 16.326 r_dihedral_angle_3_deg 13.862 r_dihedral_angle_1_deg 6.013 r_scangle_it 3.778 r_scbond_it 2.652 r_mcangle_it 1.73 r_angle_refined_deg 1.605 r_mcbond_it 1.1 r_symmetry_vdw_refined 0.327 r_nbtor_refined 0.306 r_symmetry_hbond_refined 0.247 r_nbd_refined 0.204 r_xyhbond_nbd_refined 0.171 r_chiral_restr 0.109 r_metal_ion_refined 0.098 r_bond_refined_d 0.02 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 5584 Nucleic Acid Atoms Solvent Atoms 436 Heterogen Atoms 59
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling