Experiment: 3GCY

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.99	293	Sodium Cacodylate 50mM, Calcium chloride 140mM, Spermine 1mM, pH 6.99, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 17.388	α = 90
b = 30.618	β = 90
c = 44.488	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	2009-02-14	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	1.8	30	95.9	0.1026	0.0888	4.2	4.1	2431	2334			27.37

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)
	1.8	1.86	99.1		0.3416	0.2905	1.3	4.27	226

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	1.8	15.12	2309	2216	114	95.96	0.22845	0.22812	0.23339	RANDOM	19.708

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]
-0.01			0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	2.196
r_scbond_it	2.172
r_angle_refined_deg	2.087
r_nbtor_refined	0.287
r_xyhbond_nbd_refined	0.263
r_symmetry_vdw_refined	0.247
r_nbd_refined	0.18
r_symmetry_hbond_refined	0.179
r_chiral_restr	0.067
r_bond_refined_d	0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	2.196
r_scbond_it	2.172
r_angle_refined_deg	2.087
r_nbtor_refined	0.287
r_xyhbond_nbd_refined	0.263
r_symmetry_vdw_refined	0.247
r_nbd_refined	0.18
r_symmetry_hbond_refined	0.179
r_chiral_restr	0.067
r_bond_refined_d	0.01
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	246
Solvent Atoms	36
Heterogen Atoms

Software

Software
Software Name	Purpose
MAR345dtb	data collection
PHASER	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.