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Crystal Structure c-terminal SH3 domain of Myosin IB from Entamoeba histolytica bound to EhFP10(GEF) peptide.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XGG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 0.2M Ammonium sulphate, 30% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.66 53.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.008 α = 90 b = 60.013 β = 90 c = 95.305 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD MARRESEARCH 2015-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) CC (Half) 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 1.98 50.78 100 0.103 0.103 0.9 27.76 14 12177
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 2.01 0.98 3.3
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 5xgg 1.98 50.78 11543 596 99.69 0.20307 0.20126 0.2103 0.24009 0.2504 RANDOM 38.87
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] 1.67 0.78 -2.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.656 r_dihedral_angle_4_deg 36.996 r_dihedral_angle_3_deg 15.526 r_scangle_other 14.073 r_long_range_B_refined 12.742 r_long_range_B_other 12.737 r_scbond_it 10.068 r_scbond_other 10.061 r_dihedral_angle_1_deg 6.101 r_mcangle_it 5.487
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.656 r_dihedral_angle_4_deg 36.996 r_dihedral_angle_3_deg 15.526 r_scangle_other 14.073 r_long_range_B_refined 12.742 r_long_range_B_other 12.737 r_scbond_it 10.068 r_scbond_other 10.061 r_dihedral_angle_1_deg 6.101 r_mcangle_it 5.487 r_mcangle_other 5.482 r_mcbond_it 3.88 r_mcbond_other 3.851 r_angle_refined_deg 1.87 r_angle_other_deg 1.035 r_chiral_restr 0.126 r_bond_refined_d 0.019 r_gen_planes_refined 0.012 r_bond_other_d 0.007 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1090 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing