Experiment: 3QYM

Structure of p63 DNA Binding Domain in Complex with a 10 Base Pair A/T Rich Response Element Half Site

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	298	10% PEG3350, 0.2 M ammonium formate, 0.1 M Bis-Tris, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.872	α = 90
b = 180.198	β = 92.62
c = 104.379	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 300 mm CCD	mirrors		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B		APS	23-ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	3.2	104.257	97.1	0.14	5.8	3	36604	36604			85.29

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	3.2	3.28	94.5		0.433	1.7	2.4	2610

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	PDB ENTRY 2ADY	3.2	19.719	1.45	36604	36593	1836	97.53	0.2463	0.245	0.2395	0.2709	0.2692	RANDOM

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]
9.6736		10.4226	-11.2551		1.5815

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	21.427
f_angle_d	1.372
f_chiral_restr	0.095
f_plane_restr	0.01
f_bond_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12057
Nucleic Acid Atoms	1616
Solvent Atoms
Heterogen Atoms	8

Software

Software
Software Name	Purpose
JBluIce-EPICS	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling