7B48 | pdb_00007b48

Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Human p53DBD-R273H mutant bound to MQ: R273H-MQ (II)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4IBS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	6.1	292	0.2M Li Acetate, 2.0% w/v Agarose, 20% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.249	α = 90
b = 72.003	β = 90.066
c = 85.233	γ = 90

Symmetry
Space Group	P 1 21 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 PILATUS3 2M		2016-07-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.87290	ESRF	ID23-2

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	2.05	39	94.2	0.114	0.136	0.073	0.986	10.18	3.1		49698

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	2.05	2.09	81.1		0.254	0.303	0.162	0.91		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	4IBS	2.05	36.67	47284	2400	93.9	0.1787	0.1762	0.19	0.2275	0.25	RANDOM	31.036

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]
-7.59		-4.02	11		-3.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.805
r_dihedral_angle_4_deg	17.704
r_dihedral_angle_3_deg	15.253
r_dihedral_angle_1_deg	8.019
r_angle_refined_deg	2.012
r_angle_other_deg	1.44
r_chiral_restr	0.097
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.805
r_dihedral_angle_4_deg	17.704
r_dihedral_angle_3_deg	15.253
r_dihedral_angle_1_deg	8.019
r_angle_refined_deg	2.012
r_angle_other_deg	1.44
r_chiral_restr	0.097
r_bond_refined_d	0.014
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	5955
Nucleic Acid Atoms
Solvent Atoms	477
Heterogen Atoms	77

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PDB_EXTRACT	data extraction
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.