9BC3

Transglutaminase 2 - Alternate state

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		truncated version of intermediate state

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	10% PEG 4K, 10% 2-propanol, 0.1 M HEPES (pH 7.0)

Crystal Properties
Matthews coefficient	Solvent content
1.57	21.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.448	α = 90.81
b = 71.416	β = 107.19
c = 77.473	γ = 94.43

Symmetry
Space Group	P 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 PILATUS 6M	Rh coated collimating mirrors, K-B focusing mirrors	2022-03-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.9795	SSRL	BL12-2

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	2.52	39.11	83.5	0.099	0.135	0.092	0.986	7.3	2.2		26716

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	2.52	2.66		82	0.416	0.567	0.383	0.708		2.2

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.52	39.11	25297	1418	83.53	0.20807	0.20501	0.26452	RANDOM	28.32

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]
-1.42	-0.09	-0.58	2.6	-0.83	-0.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.58
r_dihedral_angle_1_deg	6.834
r_dihedral_angle_2_deg	3.577
r_long_range_B_refined	2.793
r_long_range_B_other	2.762
r_mcangle_it	1.308
r_mcangle_other	1.308
r_scangle_other	1.072
r_angle_refined_deg	0.94
r_mcbond_it	0.714
r_mcbond_other	0.714
r_scbond_it	0.58
r_scbond_other	0.58
r_angle_other_deg	0.359
r_chiral_restr	0.045
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6866
Nucleic Acid Atoms
Solvent Atoms	235
Heterogen Atoms	104

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
XDS	data reduction
MOLREP	phasing