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Structure of Tau5 antibody Fab fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 12E8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 295 0.2 M NaCl, 0.1 M Bis-Tris, 25 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.374 α = 90 b = 50.408 β = 115.35 c = 75.169 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 CCD MARMOSAIC 225 mm CCD 2011-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 0.97004 EMBL/DESY, HAMBURG X12
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 1.6 67.93 93.9 0.156 10.64 7.236 54464
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 1.6 1.64 64.3 1.6 1.22 6.69
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 THROUGHOUT 12E8 1.6 67.93 51747 2736 94.07 0.14502 0.14259 0.1564 0.19109 0.2002 RANDOM 18.284
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] -0.4 -0.21 -0.02 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.073 r_sphericity_free 31.698 r_dihedral_angle_4_deg 17.547 r_dihedral_angle_3_deg 11.841 r_sphericity_bonded 8.527 r_dihedral_angle_1_deg 6.324 r_long_range_B_refined 4.089 r_long_range_B_other 4.089 r_rigid_bond_restr 3.059 r_scangle_other 2.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.073 r_sphericity_free 31.698 r_dihedral_angle_4_deg 17.547 r_dihedral_angle_3_deg 11.841 r_sphericity_bonded 8.527 r_dihedral_angle_1_deg 6.324 r_long_range_B_refined 4.089 r_long_range_B_other 4.089 r_rigid_bond_restr 3.059 r_scangle_other 2.99 r_scbond_it 2.591 r_scbond_other 2.586 r_mcangle_it 2.508 r_mcangle_other 2.508 r_mcbond_it 1.912 r_mcbond_other 1.909 r_angle_refined_deg 1.364 r_angle_other_deg 0.751 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 3369 Nucleic Acid Atoms Solvent Atoms 343 Heterogen Atoms 125
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing