Experiment: 3GDA

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.99	293	Sodium cacodylate 50mM, SnCl2 0.5mM, Spermine 10mM, Methyl pentane diol 33%, pH 6.99, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 17.552	α = 90
b = 30.207	β = 90
c = 43.682	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	IMAGE PLATE	MAR scanner 345 mm plate	mirrors	2008-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.87	12	99.1	0.0579	0.0501	6.7	4.05	2132	2113			38.47

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.87	1.94	98.6		0.332	0.2838	1.1	4.18	206

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	THROUGHOUT	Z-DNA FIBER MODEL BUILT WITH INSIGHT-II	1.88	10.92	1999	1992	107	99.62	0.24219	0.241	0.26596	RANDOM	25.051

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]
0.09			-0.11		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_scbond_it	2.676
r_scangle_it	2.675
r_angle_refined_deg	2.015
r_nbtor_refined	0.282
r_symmetry_vdw_refined	0.277
r_symmetry_hbond_refined	0.203
r_nbd_refined	0.162
r_xyhbond_nbd_refined	0.158
r_chiral_restr	0.073
r_bond_refined_d	0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_scbond_it	2.676
r_scangle_it	2.675
r_angle_refined_deg	2.015
r_nbtor_refined	0.282
r_symmetry_vdw_refined	0.277
r_symmetry_hbond_refined	0.203
r_nbd_refined	0.162
r_xyhbond_nbd_refined	0.158
r_chiral_restr	0.073
r_bond_refined_d	0.011
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	240
Solvent Atoms	19
Heterogen Atoms

Software

Software
Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
REFMAC	refinement
AUTOMAR	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 R01GM133198.