9S9M | pdb_00009s9m

Crystal structure of p53 cancer mutant Y220C in complex with rezatapopt analog 7

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	mM Hepes, pH 7.0, 19% (w/v) polyethylene glycol 4000. Soaking buffer: 19 mM compound in 100 mM Hepes, pH 7.2, 10 mM sodium phosphate, pH 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mM KCl.

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.832	α = 90
b = 71.037	β = 90
c = 104.564	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		2024-08-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97627	Diamond	I04

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	1.83	71.04	100	0.074	0.999	17.5	13.7		43365			31.95

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	1.83	1.87	100		1.622	0.895	1.9	14.1

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	1.83	55.1	1.33788785473	43169	2081	99.6583327562	0.193214583308	0.191622997646	0.1961	0.225517227347	0.2276	39.7950390633

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	10.8646570105
f_angle_d	0.804726541856
f_chiral_restr	0.0541165895335
f_plane_restr	0.00714947451178
f_bond_d	0.00646083318894

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3029
Nucleic Acid Atoms
Solvent Atoms	286
Heterogen Atoms	86

Software

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