9S9P | pdb_00009s9p

Crystal structure of p53 cancer mutant Y220S 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: 0.2 M ammonium nitrate, 20% PEG 3350 (protein:buffer 2:1). Cryo: reservoir buffer supplemented with 23% ethylene glycol.

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.78	α = 90
b = 70.991	β = 90
c = 104.645	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 XE 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)	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	1.4	55.1	99.5	0.066	0.999	16.2	9.4		95141			14.86

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	1.4	1.42	94		0.71	0.759	2	6.3

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	1.4	47.9	1.35017416071	94982	4852	99.4034661755	0.163011235977	0.161605367045	0.1666	0.188399780399	0.1928	21.6974802549

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	14.2872196363
f_angle_d	0.789488454253
f_chiral_restr	0.0798825749381
f_plane_restr	0.00796126660718
f_bond_d	0.00472663866673

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3053
Nucleic Acid Atoms
Solvent Atoms	491
Heterogen Atoms	164

Software

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