5MF7

New Insights into the Role of DNA Shape on Its Recognition by p53 Proteins (complex p53DBD-GADD45)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2AC0	PDBID 2AC0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	8	292	4% Tacsimate, 12% w/v Polyethylene glycol 3,350

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 138.056	α = 90
b = 50.034	β = 92.52
c = 67.202	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	MARMOSAIC 225 mm CCD		2011-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.87260	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.48	50	98	0.102	5.3	8		75213			14.56

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	1.48	1.51	93.1		1.533	0.714		6.5

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	PDBID 2AC0	1.59	49.199	1.34	60700	4207	98.12	0.2008	0.1984	0.2332	RANDOM SELECTION	23.2305

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	18.833
f_angle_d	1.073
f_chiral_restr	0.066
f_bond_d	0.01
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2906
Nucleic Acid Atoms	574
Solvent Atoms	464
Heterogen Atoms	9

Software

Software
Software Name	Purpose
PHENIX	refinement
PHASER	phasing
HKL-2000	data collection
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction

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.