X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4Y5Vchain C residues 9-120
experimental modelPDB 4Y5Vchain C residues 122-223
experimental modelOtherresidues 1-126 and 1-127 (IMGT numbering) of Fab heavy chain and light chain, respectively, of an unpublished Fab
experimental modelOtherresidues 129-230 and 130-231 (IMGT numbering) of Fab heavy chain and light chain, respectively, of an unpublished Fab

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP52980.1 M MMT buffer pH 5.0, 25% PEG1500
Crystal Properties
Matthews coefficientSolvent content
3.0359.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.165α = 90
b = 91.612β = 90
c = 216.735γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16Mmirrors2023-04-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.979180APS24-ID-E

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.85108.3799.90.1220.1330.0520.99710.86.53488079.05
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)RedundancyNumber Unique Reflections (All)
12.852.991001.0431.1260.4230.7871.97.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.984.381.3533077158499.80.22160.21910.272779.64
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d18.6046
f_angle_d1.2174
f_chiral_restr0.0631
f_plane_restr0.0163
f_bond_d0.0097
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7894
Nucleic Acid Atoms
Solvent Atoms3
Heterogen Atoms43

Software

Software
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing