9GDG | pdb_00009gdg

Crystal structure of TRIM24 PHD-BRD in complex with N-(2-(2-(2-acetamidoethoxy)ethoxy)ethyl)-3-(N-(1,3-dimethyl-2-oxo-6-(3-propoxyphenoxy)-2,3-dihydro-1H-benzo[d]imidazol-5-yl)sulfamoyl)benzamide (PEG linker unresolved)

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3O33

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.3	293	1.8 M ammonium sulfate, 0.1 M HEPES (pH 7.3), 5% PEG400

Crystal Properties
Matthews coefficient	Solvent content
2.37	48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.942	α = 90
b = 36.652	β = 111.325
c = 65.456	γ = 90

Symmetry
Space Group	C 1 2 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 S 16M		2024-07-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	1.46	60.974	84.9	0.051	18.5	6.44		23849

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.46	1.64			0.623	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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.462	60.974	23848	1232	67.98	0.153	0.1499	0.1582	0.2098	0.2122	25.956

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]
0.043		0.032	-0.159		0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.534
r_lrange_it	18.876
r_lrange_other	18.804
r_scangle_it	17.478
r_scangle_other	17.471
r_dihedral_angle_6_deg	16.766
r_dihedral_angle_3_deg	15.374
r_scbond_it	12.517
r_scbond_other	12.512
r_mcangle_other	11.454
r_mcangle_it	11.452
r_mcbond_it	8.242
r_mcbond_other	8.198
r_rigid_bond_restr	7.386
r_dihedral_angle_1_deg	6.404
r_angle_refined_deg	2.175
r_angle_other_deg	0.779
r_nbd_other	0.314
r_nbd_refined	0.222
r_symmetry_nbd_other	0.209
r_nbtor_refined	0.196
r_symmetry_xyhbond_nbd_refined	0.165
r_chiral_restr	0.137
r_symmetry_nbd_refined	0.137
r_xyhbond_nbd_refined	0.126
r_metal_ion_refined	0.117
r_symmetry_nbtor_other	0.087
r_bond_refined_d	0.014
r_gen_planes_other	0.013
r_gen_planes_refined	0.012
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1431
Nucleic Acid Atoms
Solvent Atoms	119
Heterogen Atoms	50

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data processing
STARANISO	data scaling
PHASER	phasing
autoPROC	data reduction