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Structure of Vinculin VD1 / IpaA560-633 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SYQ pdb entry 1SYQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 100 mM HEPES, 10% 2-propanol, 20% PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3 59.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.684 α = 90 b = 68.326 β = 90 c = 96.521 γ = 90
Symmetry Space Group P 21 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 IMAGE PLATE MAR scanner 345 mm plate 2005-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B 0.8423 EMBL/DESY, HAMBURG BW7B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.74 15.19 99 0.085 0.085 7.1 4.7 9559
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.74 2.89 100 0.35 0.351 2.1 4.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 pdb entry 1SYQ 2.74 15.18 9974 9493 467 99.3 0.25 0.24966 0.247 0.2428 0.294 0.2936 RANDOM 41.51
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] -1.077 7.092 -6.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.701 r_dihedral_angle_3_deg 19.841 r_dihedral_angle_4_deg 19.459 r_dihedral_angle_1_deg 5.483 r_scangle_it 2.913 r_scbond_it 1.693 r_angle_refined_deg 1.578 r_mcangle_it 1.179 r_mcbond_it 0.685 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.701 r_dihedral_angle_3_deg 19.841 r_dihedral_angle_4_deg 19.459 r_dihedral_angle_1_deg 5.483 r_scangle_it 2.913 r_scbond_it 1.693 r_angle_refined_deg 1.578 r_mcangle_it 1.179 r_mcbond_it 0.685 r_nbtor_refined 0.308 r_nbd_refined 0.243 r_xyhbond_nbd_refined 0.192 r_symmetry_vdw_refined 0.181 r_chiral_restr 0.104 r_symmetry_hbond_refined 0.045 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1993 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CCP4 data scaling