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Crystal structure of monoclonal antibody MN423 Fab fragment with free combining site, crystallized in the presence of zinc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V17 PDB ENTRY 2V17
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 294 10% PEG 3350, 0.1M IMIDAZOLE, 0.01M ZNSO4, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.37 48.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.33 α = 90 b = 75.426 β = 92.86 c = 72.701 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 100 CCD MAR CCD 165 mm 2006-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8166 EMBL/DESY, HAMBURG X11
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 2 19.9 84.6 0.065 24684 24684 25.4
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 2 2.05 99.7 0.415 5 4.7 2203
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 2V17 2 19.9 24684 23431 1253 81.75 0.16237 0.16237 0.15789 0.1662 0.2486 0.2536 RANDOM 16.43
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] 2.39 -0.17 -1.94 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.766 r_dihedral_angle_4_deg 21.916 r_dihedral_angle_3_deg 15.35 r_dihedral_angle_1_deg 7.699 r_scangle_it 4.658 r_scbond_it 3.182 r_angle_refined_deg 2.192 r_mcangle_it 1.929 r_mcbond_it 1.182 r_angle_other_deg 1.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.766 r_dihedral_angle_4_deg 21.916 r_dihedral_angle_3_deg 15.35 r_dihedral_angle_1_deg 7.699 r_scangle_it 4.658 r_scbond_it 3.182 r_angle_refined_deg 2.192 r_mcangle_it 1.929 r_mcbond_it 1.182 r_angle_other_deg 1.109 r_mcbond_other 0.387 r_symmetry_vdw_other 0.276 r_symmetry_vdw_refined 0.22 r_nbd_other 0.212 r_nbd_refined 0.207 r_nbtor_refined 0.187 r_xyhbond_nbd_refined 0.178 r_symmetry_hbond_refined 0.156 r_metal_ion_refined 0.142 r_chiral_restr 0.135 r_nbtor_other 0.099 r_bond_refined_d 0.027 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_symmetry_metal_ion_refined
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3330 Nucleic Acid Atoms Solvent Atoms 434 Heterogen Atoms 8
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling