9GD5 | pdb_00009gd5

Crystal structure of apo TRIM24 PHD-BRD in C121 space group

X-RAY DIFFRACTION

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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		293	2M ammonium sulfate, 0.1M HEPES (pH 7.9), 2% PEG400, 8% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.9	α = 90
b = 36.907	β = 110.044
c = 129.363	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 XE 16M		2024-02-18	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	1.68	44.45	95.7	0.144	1.97	6.5		43525

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	1.68	1.71			0.3

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	NONE	1.681	44.45	43514	2124	95.656	0.212	0.2104	0.2108	0.2402	0.2411	26.174

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]
-0.031		0.051	-0.017		0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.086
r_dihedral_angle_3_deg	13.326
r_lrange_it	6.398
r_dihedral_angle_1_deg	6.022
r_scangle_it	5.171
r_dihedral_angle_2_deg	4.763
r_scbond_it	3.389
r_mcangle_it	3.349
r_mcbond_it	2.327
r_angle_refined_deg	1.602
r_nbtor_refined	0.306
r_symmetry_nbd_refined	0.225
r_nbd_refined	0.205
r_symmetry_xyhbond_nbd_refined	0.152
r_xyhbond_nbd_refined	0.14
r_metal_ion_refined	0.128
r_ncsr_local_group_1	0.108
r_chiral_restr	0.104
r_bond_refined_d	0.009
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2878
Nucleic Acid Atoms
Solvent Atoms	130
Heterogen Atoms	4

Software

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