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Yeast Myo5 SH3 domain, tetragonal crystal form
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 sodium malonate, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.3 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.62 α = 90 b = 34.62 β = 90 c = 99.48 γ = 90
Symmetry Space Group P 41 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 CCD MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.81 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 1.68 20 96.8 0.053 17.6 5 7261 7261 -3 -3 26
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 1.68 1.75 99.6 0.422 3.7 4.9 824
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 MOLECULAR REPLACEMENT THROUGHOUT 1.68 20 -3 7259 7259 363 96.89 0.19156 0.19156 0.18997 0.197 0.22235 0.2299 RANDOM 22.21
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] 1.01 1.01 -2.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 27.177 r_dihedral_angle_2_deg 20.227 r_dihedral_angle_3_deg 9.87 r_dihedral_angle_1_deg 5.376 r_scangle_it 2.022 r_scbond_it 1.573 r_mcangle_it 1.163 r_angle_refined_deg 1.162 r_mcbond_it 0.987 r_angle_other_deg 0.731
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 27.177 r_dihedral_angle_2_deg 20.227 r_dihedral_angle_3_deg 9.87 r_dihedral_angle_1_deg 5.376 r_scangle_it 2.022 r_scbond_it 1.573 r_mcangle_it 1.163 r_angle_refined_deg 1.162 r_mcbond_it 0.987 r_angle_other_deg 0.731 r_symmetry_vdw_refined 0.243 r_nbd_other 0.241 r_symmetry_vdw_other 0.209 r_nbd_refined 0.189 r_mcbond_other 0.176 r_xyhbond_nbd_refined 0.17 r_symmetry_hbond_refined 0.132 r_nbtor_other 0.083 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 450 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing