8OXW

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

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Other structure in paper

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.1	298	0.1M HEPES-MOPS pH 7.1, 22% ethylene glycol, 11% PEG8000, 10 mM CaCl2, 10 mM MgCl2

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.505	α = 90
b = 93.488	β = 92.632
c = 90.644	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 4M		2022-05-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.9677	ESRF	MASSIF-3

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.7	50.02	98.7	0.059	0.083	0.058	0.995	7.1	3		146920

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)	Redundancy	Number Unique Reflections (All)
1	1.7	1.73			1.024	1.436	1.005	0.359		2.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.7	45.315	146656	7468	98.422	0.174	0.1724	0.2101	33.026

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]
-0.43		-0.277	1.752		-1.291

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.52
r_dihedral_angle_3_deg	14.285
r_lrange_it	8.73
r_lrange_other	8.647
r_dihedral_angle_2_deg	8.264
r_dihedral_angle_1_deg	7.61
r_scangle_it	6.192
r_scangle_other	6.191
r_mcangle_it	4.786
r_mcangle_other	4.786
r_scbond_it	4.267
r_scbond_other	4.266
r_mcbond_it	3.382
r_mcbond_other	3.381
r_angle_refined_deg	1.733
r_angle_other_deg	0.594
r_metal_ion_refined	0.274
r_symmetry_nbd_refined	0.255
r_nbd_refined	0.198
r_nbd_other	0.196
r_symmetry_nbd_other	0.195
r_xyhbond_nbd_refined	0.19
r_symmetry_xyhbond_nbd_refined	0.188
r_nbtor_refined	0.179
r_symmetry_xyhbond_nbd_other	0.105
r_symmetry_nbtor_other	0.088
r_chiral_restr	0.085
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8615
Nucleic Acid Atoms
Solvent Atoms	1151
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
Coot	model building
PHASER	phasing
DIALS	data reduction