☰ Navigation Tabs
Crystal Structure of the Fab fragment of humanized 5c8 antibody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I9R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 273 33% PEG 3350, 0.1 M Citric Acid/Sodium Citrate pH 4.0
Crystal Properties Matthews coefficient Solvent content 2.09 41.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.894 α = 90 b = 60.305 β = 96.27 c = 73.456 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 PIXEL DECTRIS PILATUS3 6M 2016-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97934 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.77 50.16 98.1 0.052 0.057 0.022 11.1 6.3 38013
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.77 1.8 94.4 0.324 0.356 0.143 0.936 5.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1i9r 1.77 50.16 36102 1853 98.24 0.171 0.1693 0.1787 0.2042 0.2133 RANDOM 24.955
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] -0.09 0.05 0.21 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.406 r_dihedral_angle_4_deg 22.575 r_dihedral_angle_3_deg 12.34 r_dihedral_angle_1_deg 8.671 r_angle_refined_deg 1.758 r_angle_other_deg 0.953 r_chiral_restr 0.1 r_bond_refined_d 0.015 r_gen_planes_refined 0.003 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.406 r_dihedral_angle_4_deg 22.575 r_dihedral_angle_3_deg 12.34 r_dihedral_angle_1_deg 8.671 r_angle_refined_deg 1.758 r_angle_other_deg 0.953 r_chiral_restr 0.1 r_bond_refined_d 0.015 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3205 Nucleic Acid Atoms Solvent Atoms 271 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction