4C63 | pdb_00004c63

ULTRA HIGH RESOLUTION DICKERSON-DREW DODECAMER B-DNA WITH 5- METHYLCYSTOSINE MODIFICATION

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BNA	PDB ENTRY 1BNA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		40% MPD, SPERMINE, MAGNESIUM CHLORIDE, SODIUM CACODYLATE PH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.02	39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 24.456	α = 90
b = 40.06	β = 90
c = 65.414	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	PIXEL	DECTRIS PILATUS 2M	MIRRORS	2011-08-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1		Diamond	I04-1

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	1.3	25.34	98.4	0.06	18	12.4		16355			19.15

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	1.3	1.37	93.9		1.23	2.3	12.4

Refinement

Statistics
Diffraction ID	Structure Solution 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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 1BNA	1.32	25.335	15039	1503	95.57	0.1534	0.1497	0.15	0.1848	0.19	24.89

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]
2.8962			-1.8127		-1.0835

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	31.124
f_angle_d	2.364
f_chiral_restr	0.113
f_plane_restr	0.033
f_bond_d	0.021

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	488
Solvent Atoms	94
Heterogen Atoms	1

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	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.