9EK5 | pdb_00009ek5

TRIM21 PrySpry domain bound to an enhanced PRLX-93936 analog

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-P19474-F1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		289	4.2 M Sodium Formate; 100 mM Tris-HCl, pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
3.03	59.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.317	α = 90
b = 99.317	β = 90
c = 50.403	γ = 90

Symmetry
Space Group	P 41 21 2

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		2024-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.97946	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.84	99.32	99.8	0.998	7.4	26.1		22542

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.93	100		0.344

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	2.1	70.326	14428	731	94.753	0.199	0.1953	0.2061	0.2647	0.2678	62.801

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]
-3.012			-3.012		6.024

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.912
r_dihedral_angle_3_deg	16.508
r_lrange_it	13.934
r_lrange_other	13.933
r_dihedral_angle_6_deg	13.88
r_scangle_it	9.98
r_scangle_other	9.976
r_dihedral_angle_1_deg	8.491
r_mcangle_it	8.067
r_mcangle_other	8.066
r_scbond_it	6.374
r_scbond_other	6.371
r_mcbond_it	5.449
r_mcbond_other	5.385
r_angle_refined_deg	1.507
r_angle_other_deg	0.517
r_symmetry_xyhbond_nbd_refined	0.252
r_nbd_other	0.212
r_nbd_refined	0.208
r_symmetry_nbd_other	0.206
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.181
r_symmetry_nbd_refined	0.146
r_symmetry_nbtor_other	0.089
r_chiral_restr	0.073
r_chiral_restr_other	0.032
r_gen_planes_refined	0.007
r_bond_refined_d	0.006
r_symmetry_xyhbond_nbd_other	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1449
Nucleic Acid Atoms
Solvent Atoms	71
Heterogen Atoms	29

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing