Experiment: 1S9B

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	Other		ideal B-DNA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	MPD, Nickel Chloride, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.47	64.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.867	α = 90
b = 70.867	β = 90
c = 70.867	γ = 90

Symmetry
Space Group	I 2 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1		CCD	MARRESEARCH		2002-09-10
2	1	x-ray		CCD	MARRESEARCH		2002-09-10	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	1.00000	ESRF	BM14
2	SYNCHROTRON	ESRF BEAMLINE BM14	1.48475, 1.48563, 1.31155	ESRF	BM14

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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
2	2.81	22.4	97.4	0.095				1491

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	ideal B-DNA	2.81	22.4	1388	69	95.73	0.281	0.281	0.281	0.26428	RANDOM	36.94

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	4.73
r_angle_refined_deg	3.124
r_scbond_it	2.89
r_mcbond_it	0.568
r_symmetry_vdw_refined	0.245
r_nbd_refined	0.231
r_xyhbond_nbd_refined	0.202
r_chiral_restr	0.1
r_symmetry_hbond_refined	0.078
r_bond_refined_d	0.019

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	4.73
r_angle_refined_deg	3.124
r_scbond_it	2.89
r_mcbond_it	0.568
r_symmetry_vdw_refined	0.245
r_nbd_refined	0.231
r_xyhbond_nbd_refined	0.202
r_chiral_restr	0.1
r_symmetry_hbond_refined	0.078
r_bond_refined_d	0.019
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	284
Solvent Atoms	20
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHELXD	phasing
SHELXE	model building

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 R01GM133198.