2H1M | pdb_00002h1m

Synthesis, Oxidation Behavior, Crystallization and Structure of 2'-Methylseleno Guanosine Containing RNAs

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Similar RNA structure from the crystal grown in different conditions.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	293	1.0 M Li2SO4, 0.1 M Na-citrate pH 5.6, 0.5 M ((NH4))2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.314	α = 90
b = 46.314	β = 90
c = 128.348	γ = 120

Symmetry
Space Group	H 3

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	ADSC QUANTUM 315		2005-10-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	0.978948	NSLS	X25

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.9	20	97.2	0.112	12.7		2227	2227

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	3	99.5		0.32	6.5		221

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	Similar RNA structure from the crystal grown in different conditions.	2.9	20	2227	2118	102	97.24	0.21352	0.21352	0.21225	0.2176	0.2386	0.2324	RANDOM	35.247

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]
0.86	0.43		0.86		-1.29

RMS Deviations
Key	Refinement Restraint Deviation
r_angle_refined_deg	1.125
r_scangle_it	0.922
r_scbond_it	0.471
r_nbtor_refined	0.269
r_nbd_refined	0.154
r_xyhbond_nbd_refined	0.134
r_symmetry_vdw_refined	0.108
r_symmetry_hbond_refined	0.081
r_chiral_restr	0.047
r_bond_refined_d	0.005
r_gen_planes_refined	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	680
Solvent Atoms
Heterogen Atoms	15

Software

Software
Software Name	Purpose
REFMAC	refinement
CBASS	data collection
HKL-2000	data scaling
MOLREP	phasing