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Structure of MEDI8852 Fab Fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HOT 3HOT (chain B) 4KMT (chain L) experimental model PDB 4KMT 3HOT (chain B) 4KMT (chain L)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20% PEG3350, 0.2 M Ammonium Dihydrogen Phosphate, seeded from crystals obtained from 18% PEG8000, 0.1 M Sodium Cacodylate pH 6.5 and 0.2 M Calcium Acetate
Crystal Properties Matthews coefficient Solvent content 2.65 53.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.22 α = 90 b = 109.92 β = 90 c = 139.89 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 PIXEL DECTRIS PILATUS3 6M 2014-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97941 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.9 86.43 97.3 0.098 0.995 10 4.1 77785 -3 31.51
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 1.9 1.95 98.4 0.745 2.41
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 3HOT (chain B) 4KMT (chain L) 1.9 86.43 73943 3842 97.26 0.188 0.1866 0.1941 0.2171 0.2233 RANDOM 29.378
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] -0.6 1.5 -0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.471 r_dihedral_angle_4_deg 18.436 r_dihedral_angle_3_deg 12.563 r_dihedral_angle_1_deg 6.623 r_mcangle_it 2.534 r_mcbond_it 1.721 r_mcbond_other 1.701 r_angle_refined_deg 1.53 r_angle_other_deg 1.157 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.471 r_dihedral_angle_4_deg 18.436 r_dihedral_angle_3_deg 12.563 r_dihedral_angle_1_deg 6.623 r_mcangle_it 2.534 r_mcbond_it 1.721 r_mcbond_other 1.701 r_angle_refined_deg 1.53 r_angle_other_deg 1.157 r_chiral_restr 0.089 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6548 Nucleic Acid Atoms Solvent Atoms 559 Heterogen Atoms 15
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing