258D

FACTORS AFFECTING SEQUENCE SELECTIVITY ON NOGALAMYCIN INTERCALATION: THE CRYSTAL STRUCTURE OF D(TGTACA)-NOGALAMYCIN

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	182D	NDB ENTRY DDF049 (PDB: 182D)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K

Crystal Properties
Matthews coefficient	Solvent content
3.17	61.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 26.3	α = 90
b = 51.98	β = 90
c = 67.08	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	277	IMAGE PLATE	HENDRIX-LENTFER		1994-07-01	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X31		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	1.58	10.69	94	0.046		6.3		13148		1

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)
	1.58	1.66	69.5		0.196		3.6

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 (All)	R-Factor (Observed)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	NDB ENTRY DDF049 (PDB: 182D)	1.58	10.69	12358	12358	1235	94	0.192	0.188	0.188	0.237	21.78

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
s_non_zero_chiral_vol	0.091
s_from_restr_planes	0.089
s_approx_iso_adps	0.057
s_similar_dist	0.023
s_similar_adp_cmpnt	0.022
s_bond_d	0.015
s_rigid_bond_adp_cmpnt	0.004
s_angle_d
s_zero_chiral_vol
s_anti_bump_dis_restr

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	480
Solvent Atoms	97
Heterogen Atoms	247

Software

Software
Software Name	Purpose
AMoRE	phasing
SHELXL-93	refinement
DENZO	data reduction
CCP4	data scaling

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.