8OXV

Transglutaminase 3 zymogen in complex with DH patient-derived Fab DH63-B02


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NUG 
in silico modelAlphaFoldFab

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.12980.1M HEPES-MOPS pH7.1, 15% ethylene glycol, 7.5% PEG8000, 6 mM CaCl2, 6 mM MgCl2. 20% Ethylene glycol in the cryo solution.
Crystal Properties
Matthews coefficientSolvent content
2.8556.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.659α = 90
b = 94.04β = 93.463
c = 91.143γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2022-02-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.8731ESRFID23-2

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
11.841.80699.90.0960.1220.0740.9876.74.5127215
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)
11.81.831.1671.5130.9520.4573.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.841.806127154632699.910.1880.18540.22933.842
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]
-0.155-0.5270.379-0.159
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg17.098
r_dihedral_angle_3_deg14.769
r_dihedral_angle_2_deg9.942
r_lrange_it8.829
r_lrange_other8.725
r_dihedral_angle_1_deg7.774
r_scangle_it5.48
r_scangle_other5.479
r_mcangle_it4.645
r_mcangle_other4.645
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg17.098
r_dihedral_angle_3_deg14.769
r_dihedral_angle_2_deg9.942
r_lrange_it8.829
r_lrange_other8.725
r_dihedral_angle_1_deg7.774
r_scangle_it5.48
r_scangle_other5.479
r_mcangle_it4.645
r_mcangle_other4.645
r_scbond_it3.64
r_scbond_other3.64
r_mcbond_it3.135
r_mcbond_other3.135
r_angle_refined_deg1.712
r_angle_other_deg0.578
r_xyhbond_nbd_refined0.21
r_nbd_refined0.201
r_symmetry_nbd_other0.199
r_symmetry_xyhbond_nbd_refined0.186
r_metal_ion_refined0.181
r_nbtor_refined0.18
r_symmetry_nbd_refined0.173
r_nbd_other0.161
r_symmetry_nbtor_other0.088
r_chiral_restr0.083
r_symmetry_xyhbond_nbd_other0.016
r_bond_refined_d0.011
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8632
Nucleic Acid Atoms
Solvent Atoms1346
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
DIALSdata reduction
PHASERphasing
Cootmodel building
BUCCANEERmodel building