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Crystal structure of afadin PDZ domain in complex with the C-terminal peptide from nectin-3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FE5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.51 50.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.477 α = 90 b = 90.481 β = 90 c = 88.745 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD ADSC QUANTUM 315r 2010-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1 Photon Factory BL-17A
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 2.78 50 0.055 31.5 5.1 5641 5357 3
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 2.78 2.85 94.1 0.21 6.246 4.7 255
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 2FE5 2.78 47.29 5357 255 95.26 0.24133 0.24032 0.2366 0.26336 0.2617 RANDOM 67.671
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] 6.75 -1.88 -4.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.847 r_dihedral_angle_3_deg 18.526 r_dihedral_angle_4_deg 16.259 r_dihedral_angle_1_deg 6.37 r_scangle_it 4.699 r_scbond_it 2.496 r_mcangle_it 2.226 r_angle_refined_deg 1.274 r_mcbond_it 1.155 r_chiral_restr 0.065
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.847 r_dihedral_angle_3_deg 18.526 r_dihedral_angle_4_deg 16.259 r_dihedral_angle_1_deg 6.37 r_scangle_it 4.699 r_scbond_it 2.496 r_mcangle_it 2.226 r_angle_refined_deg 1.274 r_mcbond_it 1.155 r_chiral_restr 0.065 r_bond_refined_d 0.01 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1426 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection BALBES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling