8OXY

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

X-RAY DIFFRACTION

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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	8.5	298	0.1 M Bicine-Tris pH 8.5, 22% Ethylene glycol, 11% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.022	α = 90
b = 92.275	β = 92.31
c = 90.359	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 EIGER2 X 16M		2023-01-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.8856	ESRF	ID23-1

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2	60.43	99.9	0.112	0.151	0.1	0.992	5.5	3.7		88598

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	2	2.04			0.92	1.231	0.812	0.599		3.7

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	2	58.765	88561	4529	99.873	0.178	0.1758	0.2261	33.537

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		-0.236	1.435		0.155

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.192
r_dihedral_angle_3_deg	15.041
r_dihedral_angle_2_deg	8.678
r_lrange_it	8.588
r_lrange_other	8.491
r_dihedral_angle_1_deg	7.899
r_scangle_it	6.119
r_scangle_other	6.108
r_mcangle_it	4.383
r_mcangle_other	4.383
r_scbond_it	4.083
r_scbond_other	3.958
r_mcbond_it	2.886
r_mcbond_other	2.886
r_angle_refined_deg	1.663
r_angle_other_deg	0.563
r_symmetry_xyhbond_nbd_refined	0.231
r_xyhbond_nbd_refined	0.224
r_nbd_other	0.216
r_nbd_refined	0.205
r_symmetry_nbd_other	0.202
r_nbtor_refined	0.183
r_symmetry_nbd_refined	0.179
r_symmetry_xyhbond_nbd_other	0.11
r_symmetry_nbtor_other	0.09
r_chiral_restr	0.075
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8600
Nucleic Acid Atoms
Solvent Atoms	829
Heterogen Atoms	49

Software

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