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Vinculin tail bound to paxillin LD2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QKR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 295 1.26 M (NH4)2SO4, 0.2 M NaCl, 0.1 M Na Acetate pH4.5
Crystal Properties Matthews coefficient Solvent content 3.14 60.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.382 α = 90 b = 70.562 β = 131.25 c = 117.372 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 PILATUS 6M 2023-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979264 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.54 44.87 99.6 0.102 0.124 0.069 0.995 7.3 3.1 35621
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.69 99.9 0.856 1.035 0.575 0.611 3.1
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 MOLECULAR REPLACEMENT THROUGHOUT 2.54 44.87 34219 1677 99.28 0.22675 0.22522 0.2326 0.25909 0.2611 RANDOM 70.105
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] -0.04 0.2 -0.14 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.444 r_long_range_B_refined 6.077 r_long_range_B_other 6.076 r_dihedral_angle_2_deg 4.812 r_dihedral_angle_1_deg 4.675 r_scangle_other 1.152 r_angle_refined_deg 0.996 r_mcangle_other 0.879 r_mcangle_it 0.878 r_scbond_it 0.849
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.444 r_long_range_B_refined 6.077 r_long_range_B_other 6.076 r_dihedral_angle_2_deg 4.812 r_dihedral_angle_1_deg 4.675 r_scangle_other 1.152 r_angle_refined_deg 0.996 r_mcangle_other 0.879 r_mcangle_it 0.878 r_scbond_it 0.849 r_scbond_other 0.849 r_mcbond_it 0.547 r_mcbond_other 0.502 r_angle_other_deg 0.369 r_chiral_restr 0.044 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001 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 5743 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement SCALA data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction