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Crystal structure of the Fab fragment of anti-CD20 antibody Ofatumumab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U6A PDB ENTRY 1U6A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.3 277 0.2 M zinc acetate, 20% PEG3350, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.75 55.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.33 α = 90 b = 55.944 β = 122.17 c = 79.78 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2008-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.2 20 99.4 0.083 0.083 7 5.1 26208 26051 35
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.2 2.28 99.4 0.325 0.325 2.1 4.8 2618
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 ENTRY 1U6A 2.2 20 25899 24611 1288 99.42 0.19752 0.19752 0.19477 0.1971 0.24957 0.1973 RANDOM 28.506
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] -0.24 -0.17 1.2 -1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.65 r_dihedral_angle_4_deg 24.796 r_dihedral_angle_3_deg 15.682 r_dihedral_angle_1_deg 6.977 r_sphericity_free 3.956 r_scangle_it 2.318 r_scbond_it 1.563 r_angle_refined_deg 1.375 r_sphericity_bonded 1.337 r_mcangle_it 1.175
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.65 r_dihedral_angle_4_deg 24.796 r_dihedral_angle_3_deg 15.682 r_dihedral_angle_1_deg 6.977 r_sphericity_free 3.956 r_scangle_it 2.318 r_scbond_it 1.563 r_angle_refined_deg 1.375 r_sphericity_bonded 1.337 r_mcangle_it 1.175 r_rigid_bond_restr 1.144 r_mcbond_it 0.696 r_symmetry_vdw_refined 0.315 r_nbtor_refined 0.3 r_symmetry_metal_ion_refined 0.294 r_nbd_refined 0.196 r_xyhbond_nbd_refined 0.138 r_symmetry_hbond_refined 0.095 r_chiral_restr 0.093 r_metal_ion_refined 0.053 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3261 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms 3
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling