5JZQ | pdb_00005jzq

Ultrahigh-resolution centrosymmetric crystal structure of Z-DNA reveals massive presence of multiple conformations

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	292	1.5 MM WATER SOLUTION OF DNA MIXED 1:1 WITH 0.2 M (NH4)2OAc, 0.15 M Mg(OAc)2, 0.05 M HEPES SODIUM PH 7.0 AND 5% (W/V) PEG 4000 AND EQUILIBRATED AGAINST 0.5 ML of 5% (V/V) PEG 4000.

Crystal Properties
Matthews coefficient	Solvent content
1.74	28.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.3	α = 90
b = 17.61	β = 106.73
c = 36.49	γ = 90

Symmetry
Space Group	C 1 2/c 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	RAYONIX MX-225		2014-03-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.7999	BESSY	14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	0.78	38.93	95.5	0.0339	0.999	25.75	9.01		53660			12.87

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	0.78	0.8	88.4		0.403	3.12	4.54

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	AB INITIO PHASING	FREE R-VALUE	0.78	38.93	53660	982	95.5	0.1383	0.1399	0.1386	0.14	0.1425	0.13	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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
45	133	339.1

RMS Deviations
Key	Refinement Restraint Deviation
s_angle_d	1.776
s_anti_bump_dis_restr	0.1275
s_approx_iso_adps	0.1149
s_similar_adp_cmpnt	0.0652
s_bond_d	0.0169
s_from_restr_planes	0.008
s_similar_dist
s_zero_chiral_vol
s_non_zero_chiral_vol
s_rigid_bond_adp_cmpnt

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	240
Solvent Atoms	142
Heterogen Atoms	3

Software

Software
Software Name	Purpose
XDS	data reduction
XPREP	data reduction
SHELXS	phasing
SHELXL	refinement
SHELXL-97	refinement
XSCALE	data scaling
SHELX	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.