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Crystal structure of the single-chain Fv (scFv) fragment of an anti-ErbB2 antibody chA21 in complex with residues 1-192 of ErbB2 extracellular domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GJJ pdb entries 2GJJ and 2A91 experimental model PDB 2A91 pdb entries 2GJJ and 2A91
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 15% polyethylene glycol 4000, 100mM 3-(1-pyridino)-1-propane sulfonate, 100mM Na cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.97 37.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.177 α = 90 b = 87.2 β = 90 c = 108.52 γ = 90
Symmetry Space Group P 21 21 21
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 MAR CCD 165 mm 2007-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BSRF BEAMLINE 3W1A 1.000 BSRF 3W1A
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 2.45 29.91 0.072 17.3 3.6 29113 2
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 2.45 2.58 0.336 2.9 3.2 4139
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 pdb entries 2GJJ and 2A91 2.45 29.91 2 27646 1461 99.15 0.20333 0.20061 0.1994 0.25542 0.2538 RANDOM 24.493
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 0.44 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.64 r_dihedral_angle_4_deg 15.389 r_dihedral_angle_3_deg 14.717 r_dihedral_angle_1_deg 5.704 r_angle_refined_deg 1.037 r_scangle_it 0.687 r_mcangle_it 0.45 r_scbond_it 0.395 r_symmetry_vdw_refined 0.314 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.64 r_dihedral_angle_4_deg 15.389 r_dihedral_angle_3_deg 14.717 r_dihedral_angle_1_deg 5.704 r_angle_refined_deg 1.037 r_scangle_it 0.687 r_mcangle_it 0.45 r_scbond_it 0.395 r_symmetry_vdw_refined 0.314 r_nbtor_refined 0.3 r_mcbond_it 0.296 r_nbd_refined 0.178 r_symmetry_hbond_refined 0.156 r_xyhbond_nbd_refined 0.113 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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 6642 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling