Experiment: 3U89

Crystal structure of one turn of g/c rich b-dna revisited

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BD1	PDB ENTRY 1BD1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	Sodium Cacodylate, Magnesium Acetate, MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.136	α = 90
b = 25.172	β = 116.25
c = 34.094	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	120	CCD	MARMOSAIC 225 mm CCD		2003-12-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1	APS	22-ID

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	0.91	30.6	80.6	0.079	53.4	3.4		14269

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1BD1	0.96	16.06	12848	1087	92.43	0.10463	0.10291	0.1025	0.12487	0.1248	RANDOM	9.412

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]
-0.19		-0.17	-0.06		0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	2.492
r_angle_refined_deg	1.984
r_scbond_it	1.865
r_rigid_bond_restr	1.091
r_chiral_restr	0.122
r_gen_planes_refined	0.034
r_bond_refined_d	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	202
Solvent Atoms	112
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing