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Myosin II Dictyostelium discoideum motor domain S456Y bound with MgADP-AlF4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MND PDB ENTRY 1MND
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 12% PEG 8000, 50 MM HEPES PH 7, 100 MM NACL, 2 MM DTT, 2 MM NAN3
Crystal Properties Matthews coefficient Solvent content 3.1 59.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.607 α = 90 b = 151.494 β = 90 c = 154.163 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 IMAGE PLATE MARRESEARCH 2000-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A ESRF BM30A
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 76.7 89.4 0.07 20.3 5.4 63165 3
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 1.98 2.03 44.4 0.21 2.9 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 PDB ENTRY 1MND 2 76.7 59647 3117 89.4 0.195 0.194 0.2011 0.225 0.2321 RANDOM 37.25
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] -1.46 5.51 -4.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.079 r_scangle_it 3.537 r_scbond_it 2.057 r_mcangle_it 1.446 r_angle_refined_deg 1.317 r_angle_other_deg 0.818 r_mcbond_it 0.757 r_symmetry_vdw_other 0.253 r_nbd_other 0.23 r_nbd_refined 0.203
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.079 r_scangle_it 3.537 r_scbond_it 2.057 r_mcangle_it 1.446 r_angle_refined_deg 1.317 r_angle_other_deg 0.818 r_mcbond_it 0.757 r_symmetry_vdw_other 0.253 r_nbd_other 0.23 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.17 r_symmetry_hbond_refined 0.138 r_symmetry_vdw_refined 0.11 r_chiral_restr 0.106 r_nbtor_other 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5744 Nucleic Acid Atoms Solvent Atoms 389 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing