3I8D | pdb_00003i8d

The Pairing Geometry of the Hydrophobic Thymine Analog 2,4-Difluorotoluene in Duplex DNA as Analyzed by X-ray Crystallography

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3D0P	PDB ID 3D0P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	291	0.1 M NaOAc 3H2O (pH 4.6) and 8% (w/v) PEG 4000 , VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.178	α = 90
b = 66.714	β = 121.04
c = 77.571	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	MARMOSAIC 225 mm CCD		2008-11-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.9787	APS	21-ID-F

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	1.61	50	98.1	0.053	39.4	7.5	53844	52821

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	1.61	1.64			0.56	1.7	4.6	2203

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	using MOLREP	THROUGHOUT	PDB ID 3D0P	1.61	49.39	50108	2690	100	0.19929	0.19721	0.2	0.23837	0.24	RANDOM	16.68

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]
-0.58		-0.69	-0.94		0.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.772
r_dihedral_angle_3_deg	14.637
r_dihedral_angle_4_deg	14.398
r_dihedral_angle_1_deg	6.241
r_scangle_it	4.664
r_scbond_it	3.429
r_angle_refined_deg	2.536
r_mcangle_it	2.359
r_mcbond_it	1.457
r_chiral_restr	0.185

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.772
r_dihedral_angle_3_deg	14.637
r_dihedral_angle_4_deg	14.398
r_dihedral_angle_1_deg	6.241
r_scangle_it	4.664
r_scbond_it	3.429
r_angle_refined_deg	2.536
r_mcangle_it	2.359
r_mcbond_it	1.457
r_chiral_restr	0.185
r_bond_refined_d	0.03
r_gen_planes_refined	0.016

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2154
Nucleic Acid Atoms	486
Solvent Atoms	231
Heterogen Atoms	24

Software

Software
Software Name	Purpose
MAR345	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	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 R01GM157729.