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Acanthamoeba myosin I SH3 domain bound to Acan125
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DRK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.2 280 pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Crystal Properties Matthews coefficient Solvent content 27.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.969 α = 90.28 b = 37.861 β = 90.11 c = 44.506 γ = 90.64
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.86 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 1.29 25 89.4 0.02 16.6 44074
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.29 1.3 53.3 675
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2DRK 1.35 23.64 37379 1977 91.6 0.19 0.18678 0.18575 0.1953 0.20626 0.216 RANDOM 11.678
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] 0.11 -0.02 -0.1 -0.64 -0.02 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.784 r_scangle_it 2.433 r_scbond_it 1.63 r_angle_refined_deg 1.204 r_mcangle_it 1.176 r_angle_other_deg 0.767 r_mcbond_it 0.655 r_symmetry_vdw_other 0.286 r_nbd_other 0.258 r_nbd_refined 0.229
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.784 r_scangle_it 2.433 r_scbond_it 1.63 r_angle_refined_deg 1.204 r_mcangle_it 1.176 r_angle_other_deg 0.767 r_mcbond_it 0.655 r_symmetry_vdw_other 0.286 r_nbd_other 0.258 r_nbd_refined 0.229 r_symmetry_vdw_refined 0.164 r_xyhbond_nbd_refined 0.138 r_symmetry_hbond_refined 0.109 r_nbtor_other 0.089 r_chiral_restr 0.068 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.003 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2075 Nucleic Acid Atoms Solvent Atoms 269 Heterogen Atoms 64
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction AMoRE phasing