22TG | pdb_000022tg

Crystal Structure of MYST histone acetyltransferase KAT6A in complex with Compound 20

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6CT2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298.15	0.2 M Sod. Malonate, pH 6.0, 20% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.4	49.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.685	α = 90
b = 46.405	β = 90.021
c = 120.922	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	CCD	ADSC QUANTUM 210		2022-08-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	1.0	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.36	46.4	98.2	0.082	0.999	6	5.8		26843

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.36	2.45			1.2	0.696

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 (All)	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	6CT2	2.4	43.324	25600	1320	98.75	0.297	0.2927	0.2927	0.3725	0.3723	RANDOM	32.507

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]
-0.005		-0.002	-0.025		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.556
r_dihedral_angle_6_deg	14.821
r_lrange_it	8.692
r_lrange_other	8.692
r_dihedral_angle_2_deg	8.126
r_dihedral_angle_1_deg	7.858
r_scangle_it	5.776
r_scangle_other	5.776
r_mcangle_it	4.581
r_scbond_it	3.645
r_scbond_other	3.644
r_mcbond_it	2.906
r_angle_refined_deg	1.814
r_angle_other_deg	1.343
r_nbtor_refined	0.318
r_symmetry_xyhbond_nbd_refined	0.295
r_xyhbond_nbd_refined	0.289
r_nbd_refined	0.253
r_symmetry_nbd_other	0.227
r_symmetry_nbd_refined	0.168
r_chiral_restr	0.124
r_symmetry_nbtor_other	0.076
r_gen_planes_refined	0.008
r_bond_refined_d	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4265
Nucleic Acid Atoms
Solvent Atoms	121
Heterogen Atoms	64

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystFEL	data reduction
CrystalClear	data scaling
MOLREP	phasing