1EN3 | pdb_00001en3

1A CRYSTAL STRUCTURES OF B-DNA REVEAL SEQUENCE-SPECIFIC BINDING AND GROOVE-SPECIFIC BENDING OF DNA BY MAGNESIUM AND CALCIUM

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5DNB	BDJ019

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		275	INITIAL CONCENTRATION IN DROPLET: 0.24 MM DNA, 8.57 MM MAGNESIUM ACETATE, 0.11 MM STREPTONIGRIN, 10-15% MPD, 45% FINAL MPD CONCENTRATION IN RESERVOIR. SOLUTIONS WERE UNBUFFERED, VAPOR DIFFUSION, SITTING DROP, temperature 275.0K

Crystal Properties
Matthews coefficient	Solvent content
2.08	37.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.001	α = 90
b = 25.369	β = 112.98
c = 33.633	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		1998-11-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X8C		NSLS	X8C

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	0.985	8	95	0.047	21.6	5.75	13464	13464		-1	5.3

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)
	0.985	1.016	90.7		0.123	7.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	BDJ019	0.985	8	13464	13464	631	95	0.1409	0.1409	0.15	0.1592	0.17	RANDOM

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
14	114	272.84

RMS Deviations
Key	Refinement Restraint Deviation
s_approx_iso_adps	0.072
s_angle_d	0.049
s_similar_adp_cmpnt	0.026
s_anti_bump_dis_restr	0.019
s_bond_d	0.018
s_rigid_bond_adp_cmpnt	0.006
s_similar_dist
s_from_restr_planes
s_zero_chiral_vol
s_non_zero_chiral_vol

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	364
Solvent Atoms	61
Heterogen Atoms	32

Software

Software
Software Name	Purpose
X-PLOR	model building
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

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.