8OXX | pdb_00008oxx

Transglutaminase 3 in complex with inhibitor Z-don and 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 publication

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, 8 mM CaCl2, 8 mM MgCl2

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.271	α = 90
b = 65.005	β = 96.854
c = 90.908	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 9M		2022-10-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.9184	ESRF	ID30B

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	2.5	52.804	94.6	0.1	0.135	0.09	0.994	8.9	3.7		30234

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	2.5	2.6			0.576	0.776	0.516	0.79		3.9

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.5	52.804	30222	1532	94.299	0.158	0.1544	0.16	0.2221	0.22	43.41

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	-1.578		0.603

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.129
r_dihedral_angle_3_deg	16.107
r_dihedral_angle_other_3_deg	15.602
r_dihedral_angle_2_deg	13.703
r_lrange_it	9.034
r_lrange_other	9.031
r_dihedral_angle_1_deg	8.196
r_scangle_it	7.432
r_scangle_other	7.431
r_mcangle_other	6.248
r_mcangle_it	6.244
r_scbond_it	4.801
r_scbond_other	4.801
r_mcbond_it	4.076
r_mcbond_other	4.072
r_angle_refined_deg	1.652
r_angle_other_deg	0.57
r_symmetry_xyhbond_nbd_refined	0.249
r_nbd_refined	0.209
r_symmetry_nbd_other	0.208
r_nbd_other	0.185
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.169
r_metal_ion_refined	0.152
r_symmetry_nbd_refined	0.121
r_symmetry_nbtor_other	0.088
r_chiral_restr	0.073
r_ext_dist_refined_b	0.014
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6898
Nucleic Acid Atoms
Solvent Atoms	453
Heterogen Atoms	75

Software

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