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Myosin II Dictyostelium discoideum motor domain S456Y bound with MgADP-BeFx
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MMA PDB ENTRY 1MMA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 10% PEG 8000, 50 MM HEPES PH 7.0, 100 MM NACL, 2 MM DTT, 2 MM NAN3 IN THE RESERVOIR AND 7% PEG 8000, 50 MM HEPES PH 7.0, 100 MM NACL, 2 MM DTT, 2 MM NAN3 IN THE DROP
Crystal Properties Matthews coefficient Solvent content 3.2 60.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.017 α = 90 b = 186.506 β = 90 c = 54.713 γ = 90
Symmetry Space Group P 21 21 2
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 2000-04-30 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 1.75 40 96.1 0.05 20.5 4.2 105022 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 1.75 1.79 97.4 0.16 4.1 3.8
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 1MMA 1.75 40 99718 5227 96.1 0.183 0.182 0.1946 0.207 0.2174 RANDOM 22.68
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] -0.86 1.2 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.134 r_scangle_it 2.758 r_scbond_it 1.594 r_mcangle_it 1.279 r_angle_refined_deg 1.185 r_angle_other_deg 0.803 r_mcbond_it 0.669 r_symmetry_vdw_other 0.259 r_nbd_other 0.22 r_symmetry_vdw_refined 0.206
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.134 r_scangle_it 2.758 r_scbond_it 1.594 r_mcangle_it 1.279 r_angle_refined_deg 1.185 r_angle_other_deg 0.803 r_mcbond_it 0.669 r_symmetry_vdw_other 0.259 r_nbd_other 0.22 r_symmetry_vdw_refined 0.206 r_nbd_refined 0.193 r_symmetry_hbond_refined 0.174 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.097 r_nbtor_other 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 5551 Nucleic Acid Atoms Solvent Atoms 734 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing