1ZF4 | pdb_00001zf4

ATC Four-stranded DNA Holliday Junction

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZEZ	ndb entry UD0058

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	Na Cacodylate, CaCl2, Spermine, MPD in resevoir, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.936	α = 90
b = 24.034	β = 118.69
c = 40.286	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	103	CCD	MARRESEARCH		2004-02-26		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-ID-B	1.072	APS	14-ID-B

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	1.65	12.7	79.3	0.055	0.054	15.5			5414

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	1.65	1.71	48.3	32.7	0.174	0.179	3.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	ndb entry UD0058	1.65	12.7	4894	555	96.53	0.268	0.231	0.2345	0.275	0.2793	RANDOM	10.578

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]
-0.29		0.04	0.82		-0.49

RMS Deviations
Key	Refinement Restraint Deviation
r_angle_refined_deg	1.794
r_scangle_it	1.668
r_scbond_it	1.317
r_symmetry_hbond_refined	0.317
r_nbtor_refined	0.308
r_xyhbond_nbd_refined	0.289
r_nbd_refined	0.276
r_symmetry_vdw_refined	0.246
r_chiral_restr	0.07
r_bond_refined_d	0.01
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	404
Solvent Atoms	118
Heterogen Atoms	1

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
EPMR	phasing