Experiment: 7ZDD

Crystal structure of TRIM33 PHD-Bromodomain isoform B in complex with H3K10ac histone peptide.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5MR8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	295.15	0.2 M ammonium chloride, 0.1 M sodium acetate pH 5.0, 20% w/v PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.13	α = 90
b = 52.893	β = 90
c = 105.698	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	197	PIXEL	DECTRIS EIGER2 XE 16M		2021-07-05	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)	R Merge I (Observed)	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	1.625	37.385	92.2	0.098	0.043	0.998	12	6.2		16564

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.625	1.776	57.7		1.184	0.462	0.595	1.6	7.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	5MR8	1.625	37.38	16564	841	63	0.2099	0.2077	0.2012	0.2502	0.243	RANDOM	24.22

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]
0.3863			-1.2933		0.907

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	16.39
t_omega_torsion	3.19
t_angle_deg	0.86
t_bond_d	0.008
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_sum_occupancies
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1506
Nucleic Acid Atoms
Solvent Atoms	182
Heterogen Atoms	11

Software

Software
Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
STARANISO	data scaling
PHASER	phasing