6NB8

Crystal structure of anti- SARS-CoV human neutralizing S230 antibody Fab fragment


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6C5V 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION72933.5 M sodium formate
Crystal Properties
Matthews coefficientSolvent content
2.1943.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.823α = 90
b = 104.406β = 90
c = 108.71γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80PIXELDECTRIS PILATUS3 6M2018-05-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.9774ALS5.0.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.49975.30299.60.0590.0650.02616.26.169810
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5897.70.6410.6410.7290.3371.14.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6C5V1.537.6866205351499.510.130550.128510.16714RANDOM19.587
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]
0.89-1.290.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.555
r_sphericity_free28.409
r_dihedral_angle_4_deg15.809
r_sphericity_bonded14.108
r_dihedral_angle_3_deg11.758
r_dihedral_angle_1_deg7.377
r_long_range_B_refined4.018
r_long_range_B_other3.594
r_scangle_other2.929
r_mcangle_other2.371
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.555
r_sphericity_free28.409
r_dihedral_angle_4_deg15.809
r_sphericity_bonded14.108
r_dihedral_angle_3_deg11.758
r_dihedral_angle_1_deg7.377
r_long_range_B_refined4.018
r_long_range_B_other3.594
r_scangle_other2.929
r_mcangle_other2.371
r_mcangle_it2.369
r_scbond_it2.334
r_scbond_other2.305
r_mcbond_it1.813
r_mcbond_other1.807
r_angle_refined_deg1.463
r_rigid_bond_restr1.451
r_angle_other_deg1.388
r_chiral_restr0.067
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_gen_planes_other0.003
r_bond_other_d0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3442
Nucleic Acid Atoms
Solvent Atoms468
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction