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Crystal structure of anti- MERS-CoV human neutralizing LCA60 antibody Fab fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6C5V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 293 30 % (v/v) Jeffamine ED-2001 pH 7.0 and 0.1 M HEPES pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.41 48.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.725 α = 90 b = 69.575 β = 107.65 c = 93.838 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 80 PIXEL DECTRIS PILATUS3 6M 2018-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.9774 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3 39.18 99.6 0.293 0.354 0.197 0.927 3.2 3.1 17505
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 3 3.18 99.7 1.002 1.213 0.675 0.476 3.1
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 6C5V 3 39.18 16620 873 99.39 0.2307 0.22802 0.2276 0.2827 0.278 RANDOM 50.337
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] 0.37 2.29 -4.05 1.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.345 r_dihedral_angle_4_deg 12.411 r_dihedral_angle_3_deg 11.843 r_long_range_B_other 8.809 r_long_range_B_refined 8.808 r_dihedral_angle_1_deg 6.639 r_mcangle_it 6.042 r_mcangle_other 6.042 r_scangle_other 5.222 r_mcbond_it 3.554
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.345 r_dihedral_angle_4_deg 12.411 r_dihedral_angle_3_deg 11.843 r_long_range_B_other 8.809 r_long_range_B_refined 8.808 r_dihedral_angle_1_deg 6.639 r_mcangle_it 6.042 r_mcangle_other 6.042 r_scangle_other 5.222 r_mcbond_it 3.554 r_mcbond_other 3.553 r_scbond_it 3.067 r_scbond_other 3.066 r_angle_refined_deg 1.346 r_angle_other_deg 1.322 r_chiral_restr 0.052 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 6395 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction