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High-resolution structure of yeast Myo5 SH3 domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 ammonium sulfate, isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2 38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 27.06 α = 90 b = 42.25 β = 90 c = 90.91 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 100 CCD MARRESEARCH 2004-02-03 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.813 EMBL/DESY, HAMBURG X11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.39 20 99 0.04 20 6.1 21535 21535 -3 -3 23
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.39 1.43 90.6 0.393 3.3 3.8 1598
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 MAD THROUGHOUT 1.39 20 -3 21535 21535 1077 99.12 0.16829 0.16829 0.16631 0.2148 0.20581 0.247 RANDOM 24.972
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] -0.54 0.58 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.596 r_dihedral_angle_4_deg 19.445 r_dihedral_angle_3_deg 14.932 r_dihedral_angle_1_deg 7.093 r_sphericity_free 6.756 r_scangle_it 4.894 r_scbond_it 3.973 r_mcangle_it 2.913 r_mcbond_it 2.349 r_sphericity_bonded 2.215
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.596 r_dihedral_angle_4_deg 19.445 r_dihedral_angle_3_deg 14.932 r_dihedral_angle_1_deg 7.093 r_sphericity_free 6.756 r_scangle_it 4.894 r_scbond_it 3.973 r_mcangle_it 2.913 r_mcbond_it 2.349 r_sphericity_bonded 2.215 r_rigid_bond_restr 2.069 r_angle_refined_deg 1.752 r_angle_other_deg 0.829 r_mcbond_other 0.597 r_nbd_other 0.264 r_symmetry_vdw_other 0.244 r_symmetry_vdw_refined 0.238 r_symmetry_hbond_refined 0.234 r_nbd_refined 0.229 r_nbtor_refined 0.193 r_xyhbond_nbd_refined 0.193 r_chiral_restr 0.109 r_nbtor_other 0.092 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 937 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data scaling SOLVE phasing