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Crystal structure of the primary monoclonal antibody 13PL Fab' from a multiple myeloma patient
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HIL PDB ENTRY 1HIL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 295 0.1 M citric acid, pH 4.0, 1.0 M lithium chloride, 23% PEG6000, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.26 45.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.179 α = 90 b = 80.403 β = 90 c = 102.607 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 PIXEL DECTRIS PILATUS 6M 2012-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97945 SSRL BL11-1
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 1.2 63.287 95.1 0.05 27.4 6.2 126314 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.22 73.7 0.62 1.2 3.6
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 1HIL 1.2 63.287 119898 6355 95.13 0.13721 0.13585 0.16333 0.1595 RANDOM 13.771
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] -0.65 0.09 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.26 r_sphericity_free 24.898 r_dihedral_angle_4_deg 24.411 r_dihedral_angle_3_deg 9.998 r_sphericity_bonded 9.347 r_dihedral_angle_1_deg 6.656 r_rigid_bond_restr 1.555 r_angle_refined_deg 1.34 r_angle_other_deg 0.829 r_chiral_restr 0.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.26 r_sphericity_free 24.898 r_dihedral_angle_4_deg 24.411 r_dihedral_angle_3_deg 9.998 r_sphericity_bonded 9.347 r_dihedral_angle_1_deg 6.656 r_rigid_bond_restr 1.555 r_angle_refined_deg 1.34 r_angle_other_deg 0.829 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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_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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3270 Nucleic Acid Atoms Solvent Atoms 586 Heterogen Atoms 28
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling