9FKR | pdb_00009fkr

KAT6A IN COMPLEX WITH SMALL MOLECULE INHIBITOR BAY-184

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OZU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.3	298	RESERVOIR 100 MILLIMOLAR HEPES PH 7.1-7.5, 17-21% PEG 3350 (W/V). PROTEIN CONCENTRATION 7.1 MG/ML, PROTEIN PREINCUBATED WITH 4 MILLIMOLAR ACETYL-COA. DROPS MADE FROM 0.8 MICROLITER PROTEIN AND 0.8 MICROLITER RESERVOIR SOLUTION. CRYSTAL WASHED IN RESERVOIR SOLUTION, THEN COMPOUND BACKSOAKED FOR 10 DAYS AT 10 MILLIMOLAR.

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.805	α = 92.22
b = 59.921	β = 90.82
c = 65.85	γ = 103.2

Symmetry
Space Group	P 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 PILATUS 6M-F		2018-05-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.0332	PETRA III, DESY	P11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim 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	2.69	65.79	97.4	0.086	0.101	0.997	11.5	3.5		15260			68.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.69	2.85	91.6		1.188	1.307	0.606	1.09	3.4

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	2.69	44.63	14496	763	97.33	0.199	0.19703	0.2021	0.23766	0.2407	RANDOM	73.1

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]
0.49	-0.4	-0.22	-0.02	0.09	-0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.594
r_dihedral_angle_3_deg	16.842
r_dihedral_angle_4_deg	16.461
r_long_range_B_other	7.758
r_long_range_B_refined	7.753
r_dihedral_angle_1_deg	6.458
r_scangle_other	5.416
r_mcangle_it	4.833
r_mcangle_other	4.833
r_scbond_it	3.333
r_scbond_other	3.324
r_mcbond_it	2.913
r_mcbond_other	2.913
r_angle_refined_deg	1.268
r_angle_other_deg	1.032
r_chiral_restr	0.048
r_bond_refined_d	0.004
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4343
Nucleic Acid Atoms
Solvent Atoms	42
Heterogen Atoms	76

Software

Software
Software Name	Purpose
REFMAC	refinement
pointless	data scaling
XDS	data reduction
PHASER	phasing