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Crystal structure of monoclonal human anti-rhesus D Fc and IgG1 t125(yb2/0) in the presence of EDTA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3V8C PDB ENTRY 3V8C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.1 293 12.8% MPEG 5000, 21.5% ETHYLENE GLYCOL, 0.002M EDTA, 0.1 M SODIUM CACODYLATE, pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.83 56.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.38 α = 90 b = 79.12 β = 90 c = 138.91 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 CCD ADSC QUANTUM 210 MIRRORS 2004-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 2.7 50 99.4 0.09 0.1 17.56 7.8 15731 -3 44.07
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) 1 2.69 2.85 97.2 0.538 0.491 3.78 7.8
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 3V8C 2.7 41.89 15731 14943 787 100 0.255 0.251 0.2486 0.321 0.3095 RANDOM 39.73
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] -1.62 0.19 1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.681 r_dihedral_angle_3_deg 22.281 r_dihedral_angle_4_deg 22.166 r_dihedral_angle_1_deg 7.437 r_scangle_it 2.653 r_angle_refined_deg 1.795 r_scbond_it 1.565 r_mcangle_it 1.401 r_mcbond_it 0.753 r_chiral_restr 0.106
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.681 r_dihedral_angle_3_deg 22.281 r_dihedral_angle_4_deg 22.166 r_dihedral_angle_1_deg 7.437 r_scangle_it 2.653 r_angle_refined_deg 1.795 r_scbond_it 1.565 r_mcangle_it 1.401 r_mcbond_it 0.753 r_chiral_restr 0.106 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3356 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 212
Software Software Software Name Purpose DNA data collection REFMAC refinement XDS data reduction SCALA data scaling REFMAC phasing