6P4C

HyHEL10 Fab carrying four heavy chain mutations (HyHEL10-4x): L4F, Y33H, S56N, and Y58F


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3D9APDB entry 3D9A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293100 mM citrate, pH 4.2, 1 M lithium chloride, 11% w/v PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.5752.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.556α = 90
b = 40.156β = 107.57
c = 93.649γ = 90
Symmetry
Space GroupP 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-03-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.9537Australian SynchrotronMX2

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
11.8546.471000.0510.0560.0220.99916.86.642030
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)
11.851.891000.8620.9470.3860.7786

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 REPLACEMENTTHROUGHOUTPDB entry 3D9A1.8546.4739937208999.880.18980.1880.2229RANDOM38.431
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]
-1.260.272.55-1.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.393
r_dihedral_angle_4_deg25.389
r_dihedral_angle_3_deg15.267
r_dihedral_angle_1_deg7.593
r_angle_refined_deg1.783
r_angle_other_deg1.424
r_chiral_restr0.073
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.393
r_dihedral_angle_4_deg25.389
r_dihedral_angle_3_deg15.267
r_dihedral_angle_1_deg7.593
r_angle_refined_deg1.783
r_angle_other_deg1.424
r_chiral_restr0.073
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3150
Nucleic Acid Atoms
Solvent Atoms139
Heterogen Atoms7

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction