3HS1 | pdb_00003hs1

Structure of Holliday junction formed by d(CCGGTACCGG); Crystal grown with CoCl2

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JUC	PDB ID 1JUC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	1mM DNA, 50mM Sodium Cacodylate buffer, 1mM CoCl2, 10mM spermine, 50% MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.002	α = 90
b = 24.76	β = 110.62
c = 37.369	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	IMAGE PLATE	MARRESEARCH	Mirrors	2009-02-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.5418

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	2.5	28.44	92.9	0.096	0.075	4.1	2.84	1893	1864		1	63.2

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)
	2.5	2.6	90.1		0.304	0.262	1.4	3.08	172

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 (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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ID 1JUC	2.51	28.44	1864	1760	104	92.78	0.24057	0.24057	0.23971	0.24	0.25408	0.25	RANDOM	33.891

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]
-1.29		0.01	1.65		-0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_angle_refined_deg	2.828
r_scangle_it	2.527
r_scbond_it	2.479
r_nbtor_refined	0.348
r_nbd_refined	0.268
r_xyhbond_nbd_refined	0.23
r_symmetry_vdw_refined	0.179
r_symmetry_hbond_refined	0.125
r_chiral_restr	0.105
r_bond_refined_d	0.015

RMS Deviations
Key	Refinement Restraint Deviation
r_angle_refined_deg	2.828
r_scangle_it	2.527
r_scbond_it	2.479
r_nbtor_refined	0.348
r_nbd_refined	0.268
r_xyhbond_nbd_refined	0.23
r_symmetry_vdw_refined	0.179
r_symmetry_hbond_refined	0.125
r_chiral_restr	0.105
r_bond_refined_d	0.015
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	404
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 R01GM157729.