9S9Q | pdb_00009s9q

Crystal structure of p53 cancer mutant Y220N in complex with rezatapopt

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Protein solution: 6 mg/ml in 25 mM Hepes, pH 7.5, 150 mM NaCl, 0.5 mM TCEP, 1 mM Rezatapopt, 2% DMSO. Reservoir buffer: 10% PEG 8000, 8% ethylene glycol, 0.1 M HEPES pH 7.5 (protein:buffer 1:1). Cryo: reservoir buffer supplemented with 23% ethylene glycol.

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.075	α = 90
b = 71.15	β = 90
c = 104.597	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	100	PIXEL	DECTRIS EIGER2 X 16M		2024-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97628	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	1.87	52.3	99.5	0.162	0.056	0.998	8	9.1		40660			20.16

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	1.87	1.91	99.7		1.021	0.349	0.882	2.1	9.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R-VALUE	1.87	48	1.33590843288	40529	2019	99.21662709	0.198481625995	0.196188611642	0.1984	0.242505439253	0.2448	23.6218603005

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	10.0605682671
f_angle_d	0.830911371651
f_chiral_restr	0.054744207798
f_plane_restr	0.00660398396219
f_bond_d	0.00644478915802

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3045
Nucleic Acid Atoms
Solvent Atoms	355
Heterogen Atoms	119

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing