8OXY

Transglutaminase 3 without calcium in complex with DH patient-derived Fab DH63-B02


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherOther structure in paper

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52980.1 M Bicine-Tris pH 8.5, 22% Ethylene glycol, 11% PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.7254.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.022α = 90
b = 92.275β = 92.31
c = 90.359γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2023-01-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.8856ESRFID23-1

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
1260.4399.90.1120.1510.10.9925.53.788598
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)
122.040.921.2310.8120.5993.7

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-VALUE258.76588561452999.8730.1780.17580.226133.537
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]
-1.572-0.2361.4350.155
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.192
r_dihedral_angle_3_deg15.041
r_dihedral_angle_2_deg8.678
r_lrange_it8.588
r_lrange_other8.491
r_dihedral_angle_1_deg7.899
r_scangle_it6.119
r_scangle_other6.108
r_mcangle_it4.383
r_mcangle_other4.383
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.192
r_dihedral_angle_3_deg15.041
r_dihedral_angle_2_deg8.678
r_lrange_it8.588
r_lrange_other8.491
r_dihedral_angle_1_deg7.899
r_scangle_it6.119
r_scangle_other6.108
r_mcangle_it4.383
r_mcangle_other4.383
r_scbond_it4.083
r_scbond_other3.958
r_mcbond_it2.886
r_mcbond_other2.886
r_angle_refined_deg1.663
r_angle_other_deg0.563
r_symmetry_xyhbond_nbd_refined0.231
r_xyhbond_nbd_refined0.224
r_nbd_other0.216
r_nbd_refined0.205
r_symmetry_nbd_other0.202
r_nbtor_refined0.183
r_symmetry_nbd_refined0.179
r_symmetry_xyhbond_nbd_other0.11
r_symmetry_nbtor_other0.09
r_chiral_restr0.075
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8600
Nucleic Acid Atoms
Solvent Atoms829
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing
Cootmodel building
DIALSdata reduction