7HME | pdb_00007hme

PanDDA analysis group deposition -- Crystal Structure of TRIM21 in complex with Z319545618

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VOK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	4 % PEG 400, 2 M AmmSO4, 0.1 M HEPES pH 8

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.721	α = 90
b = 95.721	β = 90
c = 45.785	γ = 90

Symmetry
Space Group	I 4

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 XE 9M		2024-05-23		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92124	Diamond	I04-1

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	1.51	67.67	100	0.177	0.184	0.05	0.999	8.8	13.3		32650

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	1.51	1.54	100		4.703	4.945	1.516	0.287		10.5

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	FOURIER SYNTHESIS	THROUGHOUT	1.51	67.69	31015	1570	99.72	0.1853	0.1843	0.2007	0.2045	0.2133	RANDOM	23.72

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]
0.01			0.01		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.177
r_dihedral_angle_4_deg	18.947
r_dihedral_angle_3_deg	13.016
r_dihedral_angle_1_deg	7.101
r_mcangle_it	3.096
r_mcbond_other	1.948
r_mcbond_it	1.946
r_angle_refined_deg	1.586
r_angle_other_deg	1.371
r_chiral_restr	0.073

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.177
r_dihedral_angle_4_deg	18.947
r_dihedral_angle_3_deg	13.016
r_dihedral_angle_1_deg	7.101
r_mcangle_it	3.096
r_mcbond_other	1.948
r_mcbond_it	1.946
r_angle_refined_deg	1.586
r_angle_other_deg	1.371
r_chiral_restr	0.073
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1493
Nucleic Acid Atoms
Solvent Atoms	138
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.