3EYI | pdb_00003eyi

The crystal structure of the second Z-DNA binding domain of human DAI (ZBP1) in complex with Z-DNA

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	295	0.1M Tris-HCl pH 8.5, 31-33% PEG 4000, 200-260 mM sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
1.76	30.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 29.53	α = 90
b = 58.249	β = 90
c = 88.609	γ = 90

Symmetry
Space Group	P 21 21 21

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	MAR CCD 165 mm		2005-01-01	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	0.9795, 0.9798, 0.9721	SPring-8	BL41XU

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	1.45	50	95.8	0.075			27940	26766	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.45	1.5	84.3		0.156	8.9		2301

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MAD	THROUGHOUT	1.45	20	26420	23803	2617	94.7	0.15719	0.15719	0.15322	0.16	0.1935	0.2	RANDOM	15.757

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]
0.06			-0.23		0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.457
r_scangle_it	3.44
r_scbond_it	2.413
r_mcangle_it	1.755
r_angle_refined_deg	1.649
r_mcbond_it	0.97
r_nbd_refined	0.275
r_symmetry_hbond_refined	0.226
r_xyhbond_nbd_refined	0.224
r_symmetry_vdw_refined	0.213

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.457
r_scangle_it	3.44
r_scbond_it	2.413
r_mcangle_it	1.755
r_angle_refined_deg	1.649
r_mcbond_it	0.97
r_nbd_refined	0.275
r_symmetry_hbond_refined	0.226
r_xyhbond_nbd_refined	0.224
r_symmetry_vdw_refined	0.213
r_chiral_restr	0.091
r_bond_refined_d	0.018
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1095
Nucleic Acid Atoms	263
Solvent Atoms	351
Heterogen Atoms

Software

Software
Software Name	Purpose
MAR345dtb	data collection
autoSHARP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

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.