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Humanized anti-PEG h6.3 Fab in complex with PEG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VL9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 18% (w/v) PEG-6000, 1% (w/v) PEG-2000-methyl ether, 0.15 M lithium sulfate monohydrate, and 0.1 M citric acid
Crystal Properties Matthews coefficient Solvent content 2.88 57.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 245.365 α = 90 b = 43.574 β = 111.7 c = 110.148 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 CCD ADSC QUANTUM 315r 2020-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.26 30 99.1 0.053 14.3 3.6 50690
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 2.27 2.35 99.2 0.333 0.391 0.202 0.9 3.7
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 THROUGHOUT 6VL9 2.26 29.81 48044 2611 98.88 0.21214 0.20944 0.2174 0.26148 0.2649 RANDOM 38.145
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] 0.27 -0.1 -0.09 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.166 r_dihedral_angle_2_deg 10.565 r_dihedral_angle_1_deg 8.069 r_long_range_B_refined 7.16 r_long_range_B_other 7.158 r_scangle_other 5.308 r_mcangle_it 4.761 r_mcangle_other 4.761 r_scbond_it 3.426 r_scbond_other 3.426
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.166 r_dihedral_angle_2_deg 10.565 r_dihedral_angle_1_deg 8.069 r_long_range_B_refined 7.16 r_long_range_B_other 7.158 r_scangle_other 5.308 r_mcangle_it 4.761 r_mcangle_other 4.761 r_scbond_it 3.426 r_scbond_other 3.426 r_mcbond_it 3.172 r_mcbond_other 3.172 r_angle_refined_deg 1.494 r_angle_other_deg 0.532 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6536 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement SCALA data scaling HKL-2000 data collection MOLREP phasing