☰ Navigation Tabs
Structure of the SH3 domain of MLK3 bound to peptide generated from phage display
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SEM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.1 M Na-Phosphate, 0.1 M K-Phosphate, 0.1 M MES 6.5, 1.5 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.31 48.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64 α = 90 b = 64 β = 90 c = 35.2 γ = 120
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 MARMOSAIC 225 mm CCD 2015-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.978720 APS 21-ID-F
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 1.2 55.43 97.2 0.042 19.53 4.92 48242
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.27 83.1 0.418 2.76 2.55
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 1SEM 1.2 55.43 46672 2412 97.21 0.13865 0.13712 0.1469 0.16826 0.1753 RANDOM 21.026
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 -0.27 -0.54 1.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.606 r_sphericity_free 32.597 r_sphericity_bonded 21.62 r_dihedral_angle_4_deg 20.048 r_dihedral_angle_3_deg 12.764 r_scangle_other 11.004 r_long_range_B_refined 9.85 r_long_range_B_other 9.847 r_scbond_other 7.901 r_scbond_it 7.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.606 r_sphericity_free 32.597 r_sphericity_bonded 21.62 r_dihedral_angle_4_deg 20.048 r_dihedral_angle_3_deg 12.764 r_scangle_other 11.004 r_long_range_B_refined 9.85 r_long_range_B_other 9.847 r_scbond_other 7.901 r_scbond_it 7.9 r_rigid_bond_restr 7.214 r_dihedral_angle_1_deg 6.022 r_mcangle_other 4.326 r_mcangle_it 4.308 r_mcbond_it 3.475 r_mcbond_other 3.459 r_angle_refined_deg 3.006 r_angle_other_deg 1.585 r_chiral_restr 0.178 r_bond_refined_d 0.035 r_gen_planes_refined 0.016 r_gen_planes_other 0.008 r_bond_other_d 0.005 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1161 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing