9O0W | pdb_00009o0w

Co-crystal structure of human TREX1 in complex with an inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7TQO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	200mM KBr, 8% PEG 20K, 8% PEG 550 MME, 100mM Tris [pH 7.5]

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.698	α = 90
b = 153.693	β = 90
c = 137.471	γ = 90

Symmetry
Space Group	C 2 2 21

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		2023-02-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.97918	APS	24-ID-E

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	1.43	50	99.9	0.065	0.069	0.024	0.999	8.1	8.4		152888

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	1.43	1.45	100		0.935	0.995	0.337	0.757		8.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.43	49.11	149775	3070	99.64	0.16195	0.16156	0.18	0.18123	0.1972	RANDOM	17.512

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]
0.2			0.06		-0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.169
r_long_range_B_refined	11.142
r_long_range_B_other	10.18
r_dihedral_angle_2_deg	6.124
r_dihedral_angle_1_deg	5.824
r_mcangle_it	5.633
r_mcangle_other	5.633
r_scangle_other	5.57
r_scbond_it	3.535
r_scbond_other	3.535
r_mcbond_it	3.48
r_mcbond_other	3.479
r_rigid_bond_restr	2.06
r_angle_refined_deg	1.307
r_angle_other_deg	0.489
r_chiral_restr	0.07
r_gen_planes_refined	0.007
r_bond_refined_d	0.005
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_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4796
Nucleic Acid Atoms
Solvent Atoms	547
Heterogen Atoms	122

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
PHASER	phasing