1NQS | pdb_00001nqs

Structural Characterisation of the Holliday Junction formed by the sequence d(TCGGTACCGA) at 1.97 A

X-RAY DIFFRACTION

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.588	α = 90
b = 23.628	β = 111.15
c = 37.223	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	CCD	MARRESEARCH		2002-05-15	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)	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	1.97	34.71	99.3	0.07	0.07	6.1	7.6	3906	3877	1	1	39.038

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)
	1.97	2.08	100		0.296	0.296	6.1	5.6	549

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	1.97	34.71	1	1	3728	3691	176	99	0.22538	0.22304	0.26	0.27779	0.32	RANDOM	39.038

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]
-0.39		-1.12	2.94		-3.36

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	4.414
r_scbond_it	2.894
r_angle_refined_deg	1.982
r_angle_other_deg	1.649
r_symmetry_vdw_other	0.339
r_xyhbond_nbd_refined	0.241
r_nbd_other	0.21
r_nbd_refined	0.153
r_symmetry_hbond_refined	0.104
r_nbtor_other	0.089

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	4.414
r_scbond_it	2.894
r_angle_refined_deg	1.982
r_angle_other_deg	1.649
r_symmetry_vdw_other	0.339
r_xyhbond_nbd_refined	0.241
r_nbd_other	0.21
r_nbd_refined	0.153
r_symmetry_hbond_refined	0.104
r_nbtor_other	0.089
r_symmetry_vdw_refined	0.082
r_metal_ion_refined	0.07
r_chiral_restr	0.065
r_gen_planes_refined	0.01
r_bond_refined_d	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	404
Solvent Atoms	42
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
XTALVIEW	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.