9IT5 | pdb_00009it5

p300 KAT domain in complex with KB528

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BIY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	HM(PEGs-E9)-D6 (0.18M NH4Cl, 24% PEG 3350)

Crystal Properties
Matthews coefficient	Solvent content
2.56	52.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.4	α = 90
b = 164.933	β = 111.845
c = 56.588	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	100	PIXEL	DECTRIS PILATUS3 6M		2024-07-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	0.99999	SPring-8	BL45XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	44.302	98	0.144	10	7.1		50921

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.05			1.085

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	FREE R-VALUE	2	44.302	50870	2644	97.906	0.19	0.1878	0.1944	0.2378	0.2372	35.942

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]
-1.279		0.951	0.293		0.169

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.372
r_dihedral_angle_3_deg	11.922
r_dihedral_angle_2_deg	7.166
r_lrange_it	6.61
r_lrange_other	6.55
r_dihedral_angle_1_deg	6.512
r_scangle_it	4.867
r_scangle_other	4.866
r_mcangle_it	3.772
r_mcangle_other	3.772
r_scbond_it	3.03
r_scbond_other	3.029
r_mcbond_it	2.506
r_mcbond_other	2.505
r_angle_refined_deg	1.281
r_angle_other_deg	0.464
r_nbd_refined	0.202
r_nbd_other	0.198
r_symmetry_xyhbond_nbd_refined	0.192
r_symmetry_nbd_other	0.185
r_nbtor_refined	0.179
r_symmetry_nbd_refined	0.174
r_xyhbond_nbd_refined	0.166
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.065
r_chiral_restr_other	0.041
r_symmetry_xyhbond_nbd_other	0.018
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5380
Nucleic Acid Atoms
Solvent Atoms	478
Heterogen Atoms	92

Software

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