1JUC | pdb_00001juc

Crystal Structure Analysis of a Holliday Junction Formed by CCGGTACCGG

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	290	40 mM sodium cacodylate (pH 7.0), 12 mM spermine, 80 mM KCl, 10% (v/v) MPD equilibrated against 35% MPD with oligo concentration of 1 mM, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 290.0K

Crystal Properties
Matthews coefficient	Solvent content
3.24	62.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.871	α = 90
b = 25.364	β = 110.57
c = 37.373	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	2001-07-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X31	1.073	EMBL/DESY, HAMBURG	X31

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.35	30	96.3	0.064			4339	2387	4	2

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)
	2.35	2.43	97.3		0.267

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	2.35	34.92	2286	104	96.41	0.22841	0.22639	0.25	0.26779	0.27	RANDOM	41.349

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]
-2.92		-0.01	3.32		-0.41

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
		426

RMS Deviations
Key	Refinement Restraint Deviation
r_angle_refined_deg	2.195
r_angle_other_deg	1.463
r_xyhbond_nbd_refined	0.523
r_chiral_restr	0.518
r_nbd_other	0.329
r_nbd_refined	0.268
r_symmetry_vdw_other	0.213
r_symmetry_hbond_refined	0.204
r_nbtor_other	0.157
r_symmetry_vdw_refined	0.155
r_bond_refined_d	0.067
r_gen_planes_refined	0.033
r_xyhbond_nbd_other	0.025
r_bond_other_d	0.002
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_gen_planes_other
r_symmetry_hbond_other
r_mcbond_it
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	404
Solvent Atoms	43
Heterogen Atoms

Software

Software
Software Name	Purpose
XFIT	data reduction
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling