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Structure of the SH3 domain of MLK3 bound to peptide generated from phage display
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.1 M NaH2PO4
0.1 M KH2PO4
0.1 M MES pH 6.5
1.5 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.51 51.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.51 α = 90 b = 45.74 β = 120.88 c = 49.66 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS EIGER X 16M 2017-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.078185 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.5 42.62 90.9 9.94 1.8 44942
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 1.5 1.59 86.9 0.848 1.63 1.83
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 1.5 42.62 22557 1181 95.12 0.18938 0.18745 0.1901 0.22761 0.2287 RANDOM 28.655
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] -0.93 -0.48 -0.02 0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.146 r_dihedral_angle_4_deg 20.967 r_dihedral_angle_3_deg 12.063 r_long_range_B_refined 10.656 r_long_range_B_other 10.652 r_dihedral_angle_1_deg 7.445 r_scangle_other 5.652 r_scbond_it 4.347 r_mcangle_other 4.286 r_mcangle_it 4.284
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.146 r_dihedral_angle_4_deg 20.967 r_dihedral_angle_3_deg 12.063 r_long_range_B_refined 10.656 r_long_range_B_other 10.652 r_dihedral_angle_1_deg 7.445 r_scangle_other 5.652 r_scbond_it 4.347 r_mcangle_other 4.286 r_mcangle_it 4.284 r_scbond_other 3.772 r_mcbond_it 3.185 r_mcbond_other 3.177 r_angle_refined_deg 2.202 r_angle_other_deg 1.092 r_chiral_restr 0.119 r_bond_refined_d 0.022 r_gen_planes_refined 0.014 r_bond_other_d 0.003 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 1058 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement MOLREP phasing ARP model building