Experiment: 3DS7

Structure of an RNA-2'-deoxyguanosine complex

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1U8D	PDB 1U8D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	0.01M K-HEPES, 0.0119 M cobalt(III) hexammine, 22% PEG 2000, 0.66M ammonium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.139	α = 86.55
b = 41.83	β = 81.16
c = 64.81	γ = 89.64

Symmetry
Space Group	P 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	IMAGE PLATE	RIGAKU RAXIS IV++		2007-11-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.54

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	1.85	19.5	94	0.075	8.4	3.56	31039	29177		2	20

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)
	1.85	1.92	91.4		0.297	3.4	3.57	2822

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 1U8D	1.85	19.5	2	31039	29005	2894	93.3	0.208	0.205	0.2	0.2311	0.259	0.2713	RANDOM	34.4

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]
-1.69	0.8	-0.28	-0.76	2.34	2.44

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	17.9
c_improper_angle_d	2.58
c_angle_deg	2
c_bond_d	0.021

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	2853
Solvent Atoms	622
Heterogen Atoms	123

Software

Software
Software Name	Purpose
CNS	refinement
CrystalClear	data collection
CrystalClear	data reduction
CrystalClear	data scaling
CNS	phasing