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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 Bis-tris, PEG 3350, NaCl
Crystal Properties Matthews coefficient Solvent content 2.09 41.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.087 α = 107.79 b = 61.089 β = 113.43 c = 65.358 γ = 95.68
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) 0.88563 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 1.55 56.28 90.5 0.068 11 3.8 99734
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 1.55 1.605 89.7 0.433 2.7 3.8
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 1.55 56.28 94753 4981 90.39 0.16826 0.16627 0.1755 0.20637 0.2121 RANDOM 16.163
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] -0.13 0.04 -0.17 1 -0.26 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.68 r_dihedral_angle_4_deg 18.941 r_dihedral_angle_3_deg 12.306 r_dihedral_angle_1_deg 7.077 r_long_range_B_refined 4.61 r_long_range_B_other 4.509 r_scangle_other 3.218 r_mcangle_it 2.312 r_mcangle_other 2.312 r_scbond_it 2.205
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.68 r_dihedral_angle_4_deg 18.941 r_dihedral_angle_3_deg 12.306 r_dihedral_angle_1_deg 7.077 r_long_range_B_refined 4.61 r_long_range_B_other 4.509 r_scangle_other 3.218 r_mcangle_it 2.312 r_mcangle_other 2.312 r_scbond_it 2.205 r_scbond_other 2.205 r_angle_refined_deg 2.061 r_mcbond_it 1.562 r_mcbond_other 1.561 r_angle_other_deg 0.922 r_chiral_restr 0.125 r_bond_refined_d 0.02 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 6396 Nucleic Acid Atoms Solvent Atoms 688 Heterogen Atoms 156
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling Coot model building PHASER phasing