Experiment: 1J8L

Molecular and Crystal Structure of D(CGCAAATTMO4CGCG): the Watson-Crick Type N4-Methoxycytidine/Adenosine Base Pair in B-DNA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	355D	PDB ENTRY 355D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	MPD, spermine, magnesium acetate, sodium cacodylate, sodum chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 24.8	α = 90
b = 40.3	β = 90
c = 65.5	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	100	DIFFRACTOMETER	WEISSENBERG		2000-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-18B	1.0	Photon Factory	BL-18B

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	1.6	100	86.1	0.058		8	62759	7855

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)
	1.6	1.69	38.4		0.132	5.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 355D	1.6	10	3	6515	685		0.218	0.2271	0.258	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]
7.27			-0.96		-6.31

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	20.7
c_improper_angle_d	1.36
c_angle_deg	0.9
c_bond_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	484
Solvent Atoms	105
Heterogen Atoms	11

Software

Software
Software Name	Purpose
AMoRE	phasing
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling