7EDS | pdb_00007eds

Human p53 core domain with germline hot spot mutation M133T in complex with the natural PIG3 p53-response element and Arsenic

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2J1Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	0.1 M Tris pH 8.5-9, 17-19% PEG20000, 0.1 M MgCl2, 2 mM EDTA, 2 mM As2O3

Crystal Properties
Matthews coefficient	Solvent content
1.42	13.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 137.53	α = 90
b = 49.88	β = 93.31
c = 33.95	γ = 90

Symmetry
Space Group	C 1 2 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 EIGER X 16M		2019-05-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.97916	SSRF	BL17U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.77	46.88	98.8	0.097	0.116	0.063	0.993	9.1	3.3		22225

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.77	1.82	96.6		0.58	0.693	0.376	0.737		3.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	2J1Y	1.77	46.88	21083	1142	98.57	0.2109	0.2101	0.2	0.2265	0.22	RANDOM	53.292

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]
-13.87		-5.68	11.08		2.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.964
r_dihedral_angle_4_deg	19.378
r_dihedral_angle_3_deg	13.609
r_dihedral_angle_1_deg	6.709
r_angle_refined_deg	1.681
r_angle_other_deg	1.09
r_chiral_restr	0.122
r_bond_refined_d	0.019
r_gen_planes_refined	0.011
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.964
r_dihedral_angle_4_deg	19.378
r_dihedral_angle_3_deg	13.609
r_dihedral_angle_1_deg	6.709
r_angle_refined_deg	1.681
r_angle_other_deg	1.09
r_chiral_restr	0.122
r_bond_refined_d	0.019
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1521
Nucleic Acid Atoms	1230
Solvent Atoms	74
Heterogen Atoms	2

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.