1NVN | pdb_00001nvn

Structural Characterisation of the Holliday junction formed by the sequence CCGGTACCGG at 1.8 A

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	290	MPD, CaCl2, cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.16	42.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.38	α = 90
b = 23.79	β = 110.13
c = 37.12	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					M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.811	EMBL/DESY, HAMBURG	X11

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	1.8	34.92	98.3	0.06	16.78	3.71	5158	5158	1	1	20.904

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)
	1.8	2.1	98.4		0.2	6.06	3.73	1885

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	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	1.8	34.92	1	1	5229	4920	236	98.49	0.20872	0.20629	0.23	0.26361	0.27	RANDOM	13.443

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]
-0.44		-0.1	1.55		-1.18

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	3.269
r_scbond_it	2.111
r_angle_refined_deg	1.731
r_angle_other_deg	1.501
r_symmetry_vdw_other	0.314
r_metal_ion_refined	0.244
r_nbd_other	0.193
r_xyhbond_nbd_refined	0.175
r_nbd_refined	0.125
r_symmetry_hbond_refined	0.124

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	3.269
r_scbond_it	2.111
r_angle_refined_deg	1.731
r_angle_other_deg	1.501
r_symmetry_vdw_other	0.314
r_metal_ion_refined	0.244
r_nbd_other	0.193
r_xyhbond_nbd_refined	0.175
r_nbd_refined	0.125
r_symmetry_hbond_refined	0.124
r_symmetry_vdw_refined	0.107
r_nbtor_other	0.094
r_chiral_restr	0.053
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	404
Solvent Atoms	91
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement

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.