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Structure of the murine antibody Fab 8E3 bound to the vaccinia virus A27 peptide 101-110
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NTF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 10% PEG 3000, 200 mM magnesium chloride, 100 mM cacodylate ph 6.5
Crystal Properties Matthews coefficient Solvent content 4.23 70.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.25 α = 90 b = 118.25 β = 90 c = 198.74 γ = 120
Symmetry Space Group P 61 2 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 CCD ADSC QUANTUM 315r 2012-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.27 55.62 97.8 0.095 6.3 2.5 35641
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 2.27 2.53 98.1 0.494 2.1 2.5
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 2NTF 2.27 55.62 35641 1885 97.13 0.20399 0.20296 0.2026 0.22363 0.2236 RANDOM 33.313
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.44 r_dihedral_angle_4_deg 16.488 r_dihedral_angle_3_deg 13.485 r_dihedral_angle_1_deg 6.087 r_angle_refined_deg 1.292 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.44 r_dihedral_angle_4_deg 16.488 r_dihedral_angle_3_deg 13.485 r_dihedral_angle_1_deg 6.087 r_angle_refined_deg 1.292 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3330 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection MOSFLM data reduction SCALA data scaling PHASER phasing PDB_EXTRACT data extraction