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Crystal structure of Onartuzumab Fab in complex with MET and HGF-beta
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SHY PDB ENTRY 1SHY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 298 0.1 M sodium cacodylate pH 6.2, 20% (w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.99 58.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.191 α = 90 b = 192.228 β = 90 c = 65.585 γ = 90
Symmetry Space Group P 21 21 2
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 315 2011-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2
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 2.8 50 98.9 0.074 15.56 4 40382
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 2.8 2.9 98 0.513 1.88 3.8 3938
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 1SHY 2.8 50 38286 2027 98.87 0.21297 0.21083 0.25287 0.2468 RANDOM 52.103
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] 0.2 -1.04 0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.189 r_dihedral_angle_3_deg 15.059 r_dihedral_angle_4_deg 14.299 r_dihedral_angle_1_deg 5.957 r_scangle_it 1.735 r_angle_refined_deg 1.05 r_scbond_it 0.982 r_mcangle_it 0.858 r_mcbond_it 0.449 r_chiral_restr 0.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.189 r_dihedral_angle_3_deg 15.059 r_dihedral_angle_4_deg 14.299 r_dihedral_angle_1_deg 5.957 r_scangle_it 1.735 r_angle_refined_deg 1.05 r_scbond_it 0.982 r_mcangle_it 0.858 r_mcbond_it 0.449 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 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 9084 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 14
Software Software Software Name Purpose Blu-Ice data collection PHASES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling