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Crystal Structure C-terminal SH3 domain of Myosin IB from Entamoeba histolytica
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IIM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 2.2M ammonium sulphate, 5% v/v isopropanol
Crystal Properties Matthews coefficient Solvent content 2.56 51.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.11 α = 90 b = 77.67 β = 108.24 c = 61.83 γ = 90
Symmetry Space Group P 1 21 1
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 MARRESEARCH 2014-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.9184 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rpim I (All) 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 1.7 77.67 99.97 0.11 0.11 0.027 0.997 4.17 6.5 101866 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 99.4 0.43 0.43 0.185 0.96 4.17 6.2
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 4iim 1.72 58.79 47114 2512 99.98 0.18627 0.18458 0.1941 0.21878 0.2261 RANDOM 15.738
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] -0.38 -0.04 -0.18 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.862 r_dihedral_angle_3_deg 12.746 r_long_range_B_refined 7.762 r_long_range_B_other 6.893 r_dihedral_angle_1_deg 5.422 r_scangle_other 4.354 r_scbond_it 2.884 r_scbond_other 2.88 r_mcangle_it 2.273 r_mcangle_other 2.273
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.862 r_dihedral_angle_3_deg 12.746 r_long_range_B_refined 7.762 r_long_range_B_other 6.893 r_dihedral_angle_1_deg 5.422 r_scangle_other 4.354 r_scbond_it 2.884 r_scbond_other 2.88 r_mcangle_it 2.273 r_mcangle_other 2.273 r_angle_refined_deg 1.969 r_mcbond_it 1.534 r_mcbond_other 1.526 r_angle_other_deg 1.04 r_chiral_restr 0.13 r_bond_refined_d 0.023 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 3061 Nucleic Acid Atoms Solvent Atoms 649 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALEPACK data scaling PHASER model building