Experiment: 8DC8

Crystal structure of p53 Y220C covalently bound to azaindole KG13

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2J1X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	100 mM HEPES, 2.2M MgSO4

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.279	α = 90
b = 85.95	β = 90
c = 84.14	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	CCD	ADSC QUANTUM 315r		2021-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	1	ALS	8.2.1

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	1.72009735908	53.46	97.9	0.999	19.6	13.7		26016			16.3820548616

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	1.72009735908	1.72009735908			0.895

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	2J1X	1.72009735908	33.0612965	1.37999454432	25986	1279	97.5816748029	0.17140833784	0.169763302239	0.1703	0.204132714926	0.2046	21.5916198793

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	12.2786611548
f_angle_d	0.957972999996
f_chiral_restr	0.0563840338381
f_bond_d	0.0064557591797
f_plane_restr	0.00510862099395

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1551
Nucleic Acid Atoms
Solvent Atoms	196
Heterogen Atoms	38

Software

Software
Software Name	Purpose
Blu-Ice	data collection
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement