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Crystal structure of monoclonal antibody against neuroblastoma associated antigen.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F8T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 MES, PEG 5000, NH4SO4
Crystal Properties Matthews coefficient Solvent content 2.19 43.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.676 α = 90 b = 64.167 β = 99.46 c = 78.9 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS 6M 2013-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.0 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.4 77.83 98.96 0.0292 14.52 2 81806
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 1.4 1.45 99.87 0.176 3.98 2
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 1F8T 1.4 77.83 77703 4103 98.95 0.1894 0.18794 0.1965 0.21714 0.2243 RANDOM 15.237
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] 0.85 -1.29 -0.44 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.755 r_dihedral_angle_4_deg 20.414 r_dihedral_angle_3_deg 11.455 r_dihedral_angle_1_deg 7.239 r_long_range_B_other 4.189 r_long_range_B_refined 4.188 r_scangle_other 3.305 r_scbond_it 2.356 r_scbond_other 2.355 r_angle_refined_deg 2.261
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.755 r_dihedral_angle_4_deg 20.414 r_dihedral_angle_3_deg 11.455 r_dihedral_angle_1_deg 7.239 r_long_range_B_other 4.189 r_long_range_B_refined 4.188 r_scangle_other 3.305 r_scbond_it 2.356 r_scbond_other 2.355 r_angle_refined_deg 2.261 r_mcangle_it 2.209 r_mcangle_other 2.209 r_mcbond_it 1.614 r_mcbond_other 1.557 r_angle_other_deg 1.003 r_chiral_restr 0.137 r_bond_refined_d 0.023 r_gen_planes_refined 0.011 r_bond_other_d 0.001 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3253 Nucleic Acid Atoms Solvent Atoms 300 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling Coot model building PHASER phasing