9HKU | pdb_00009hku

Crystal structure of CREBBP histone acetyltransferase domain in complex with Acetyl-Coenzyme A

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		298	0.2 M Sodium citrate tribasic dihydrate 20 % w/v Polyethylene glycol 3350 pH 8.2

Crystal Properties
Matthews coefficient	Solvent content
3.08	60.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.622	α = 90
b = 139.928	β = 90
c = 154.571	γ = 90

Symmetry
Space Group	P 21 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 EIGER X 16M		2020-03-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.97856	SOLEIL	PROXIMA 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	2.356	154.571	94.4	0.317	0.331	0.093	0.948	7	12.3		39974

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	2.356	2.661			1.82	1.912	0.576	0.428	1.7

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.356	154.57	39974	2017	51.6	0.2476	0.2455	0.2394	0.287	0.2848	RANDOM	58.93

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]
-7.8956			11.2091		-3.3136

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	20.12
t_omega_torsion	2.82
t_angle_deg	0.94
t_bond_d	0.007
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_utility_distance
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8765
Nucleic Acid Atoms
Solvent Atoms	273
Heterogen Atoms	110

Software

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