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Crystal structure of the human derived single chain antibody fragment (scFv) 9004G in complex with Cn2 toxin from the scorpion Centruroides noxius Hoffmann
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YBR PDB ENTRY 2YBR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 1.4 M SODIUM / POTASSIUM PHOSPHATE PH 5.6
Crystal Properties Matthews coefficient Solvent content 3.11 60.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 219.709 α = 90 b = 219.709 β = 90 c = 219.709 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD MARRESEARCH MIRRORS 2010-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F APS 21-ID-F
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 1.9 54.94 100 0.08 6.3 11.5 68864 2 20.1
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 1.9 1.95 100 0.3 2.5 11.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2YBR 1.9 42.28 65369 3488 100 0.18743 0.18613 0.21212 0.192 RANDOM 24.649
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.53 r_dihedral_angle_4_deg 13.123 r_dihedral_angle_3_deg 10.476 r_scangle_it 6.695 r_dihedral_angle_1_deg 5.737 r_mcangle_it 4.936 r_scbond_it 4.771 r_mcbond_it 3.713 r_angle_refined_deg 1.116 r_chiral_restr 0.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.53 r_dihedral_angle_4_deg 13.123 r_dihedral_angle_3_deg 10.476 r_scangle_it 6.695 r_dihedral_angle_1_deg 5.737 r_mcangle_it 4.936 r_scbond_it 4.771 r_mcbond_it 3.713 r_angle_refined_deg 1.116 r_chiral_restr 0.079 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 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_mcangle_other r_scbond_other 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 4472 Nucleic Acid Atoms Solvent Atoms 568 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing