6U1T

Crystal structure of anti-Nipah virus (NiV) F 5B3 antibody Fab fragment


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6NB8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52930.2 M Magnesium chloride, 0.1 M Tris HCl, pH 8.5 and 20% PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.754.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.12α = 90
b = 95.01β = 90
c = 137.2γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80PIXELDECTRIS PILATUS3 6M2018-06-27MSINGLE 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
11.4868.699.70.080.0880.03610.25.684268
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)
11.4831.5697.80.9040.9041.0520.5230.93.6

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 REPLACEMENTTHROUGHOUT6NB81.48368.679965423899.610.1390.13720.1733RANDOM21.717
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]
-3.943.270.68
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free41.884
r_dihedral_angle_2_deg30.144
r_sphericity_bonded23.32
r_dihedral_angle_4_deg21.125
r_dihedral_angle_1_deg14.48
r_dihedral_angle_3_deg11.449
r_rigid_bond_restr3.225
r_angle_refined_deg1.22
r_angle_other_deg0.91
r_chiral_restr0.061
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free41.884
r_dihedral_angle_2_deg30.144
r_sphericity_bonded23.32
r_dihedral_angle_4_deg21.125
r_dihedral_angle_1_deg14.48
r_dihedral_angle_3_deg11.449
r_rigid_bond_restr3.225
r_angle_refined_deg1.22
r_angle_other_deg0.91
r_chiral_restr0.061
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3296
Nucleic Acid Atoms
Solvent Atoms557
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction