Experiment: 7YGI

Crystal structure of p53 DBD domain in complex with azurin

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1E67
experimental model	PDB	3KMD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		298	0.05M Na2HPO4+19.5% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 144.839	α = 90
b = 68.75	β = 99.69
c = 83.847	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	CCD	AGILENT ATLAS CCD		2021-06-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL02U1	0.987	SSRF	BL02U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.1	19.88	99.522	0.899	6.3	6.4		46000			18.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.175			0.984

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	FREE R-VALUE	3KMD, 1E67	2.1	19.876	1.35	45781	2256	96.31	0.2158	0.213	0.2134	0.2695	0.2689

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	3.404
f_angle_d	0.966
f_chiral_restr	0.056
f_bond_d	0.009
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4968
Nucleic Acid Atoms
Solvent Atoms	568
Heterogen Atoms	11

Software

Software
Software Name	Purpose
PHENIX	refinement
ADDREF	data reduction
ADDREF	data scaling
AMPLE	phasing