8OXX

Transglutaminase 3 in complex with inhibitor Z-don and DH patient-derived Fab DH63-B02


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.12980.1M Hepes-mops pH 7.1, 22% ethylene glycol, 11% PEG8000, 8 mM CaCl2, 8 mM MgCl2
Crystal Properties
Matthews coefficientSolvent content
2.3848.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.271α = 90
b = 65.005β = 96.854
c = 90.908γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 9M2022-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.9184ESRFID30B

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
12.552.80494.60.10.1350.090.9948.93.730234
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)
12.52.60.5760.7760.5160.793.9

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-VALUE2.552.80430222153294.2990.1580.15440.222143.41
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]
1.347-1.621-1.5780.603
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.129
r_dihedral_angle_3_deg16.107
r_dihedral_angle_other_3_deg15.602
r_dihedral_angle_2_deg13.703
r_lrange_it9.034
r_lrange_other9.031
r_dihedral_angle_1_deg8.196
r_scangle_it7.432
r_scangle_other7.431
r_mcangle_other6.248
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.129
r_dihedral_angle_3_deg16.107
r_dihedral_angle_other_3_deg15.602
r_dihedral_angle_2_deg13.703
r_lrange_it9.034
r_lrange_other9.031
r_dihedral_angle_1_deg8.196
r_scangle_it7.432
r_scangle_other7.431
r_mcangle_other6.248
r_mcangle_it6.244
r_scbond_it4.801
r_scbond_other4.801
r_mcbond_it4.076
r_mcbond_other4.072
r_angle_refined_deg1.652
r_angle_other_deg0.57
r_symmetry_xyhbond_nbd_refined0.249
r_nbd_refined0.209
r_symmetry_nbd_other0.208
r_nbd_other0.185
r_nbtor_refined0.184
r_xyhbond_nbd_refined0.169
r_metal_ion_refined0.152
r_symmetry_nbd_refined0.121
r_symmetry_nbtor_other0.088
r_chiral_restr0.073
r_ext_dist_refined_b0.014
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6898
Nucleic Acid Atoms
Solvent Atoms453
Heterogen Atoms75

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Cootmodel building
PHASERphasing
XDSdata reduction
Aimlessdata scaling