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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 2.87 57.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.013 α = 90 b = 147.772 β = 90 c = 153.39 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 2.2 50 99.1 0.073 10.4 5.7 50629
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) 2.2 2.28 94.8 0.224 4.5
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 2.2 50 48034 2569 99.11 0.19493 0.19224 0.1902 0.24479 0.2429 RANDOM 34.536
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] -0.3 2.7 -2.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.685 r_dihedral_angle_4_deg 18.489 r_dihedral_angle_3_deg 15.307 r_dihedral_angle_1_deg 6.278 r_scangle_it 4 r_scbond_it 2.817 r_mcangle_it 1.855 r_angle_refined_deg 1.826 r_mcbond_it 1.147 r_metal_ion_refined 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.685 r_dihedral_angle_4_deg 18.489 r_dihedral_angle_3_deg 15.307 r_dihedral_angle_1_deg 6.278 r_scangle_it 4 r_scbond_it 2.817 r_mcangle_it 1.855 r_angle_refined_deg 1.826 r_mcbond_it 1.147 r_metal_ion_refined 0.323 r_nbtor_refined 0.307 r_symmetry_hbond_refined 0.299 r_symmetry_vdw_refined 0.226 r_nbd_refined 0.211 r_xyhbond_nbd_refined 0.207 r_chiral_restr 0.123 r_bond_refined_d 0.022 r_gen_planes_refined 0.008 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 5528 Nucleic Acid Atoms Solvent Atoms 596 Heterogen Atoms 60
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