3GLP | pdb_00003glp

1.23 A resolution X-ray structure of (GCUGCUGC)2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	Other		A-form RNA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	292	MgCl2, Li2SO4, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.96	α = 90
b = 38.85	β = 89.98
c = 77.72	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	100	CCD	MAR CCD 165 mm		2007-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.808	EMBL/DESY, HAMBURG	X13

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	1.23	20	99.1	0.058	21.3	7.1	32055	32055			14.2

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	1.23	1.25	98.1		0.3	5.7	6.2	1502

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	A-RNA model	1.23	17.98	31664	30062	1602	98.77	0.184	0.148	0.147	0.149	0.184	random	22.8

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]
0.09		-0.3	0.1		-0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	12.127
r_sphericity_bonded	9.17
r_scangle_it	4.008
r_scbond_it	3.418
r_angle_refined_deg	2.749
r_rigid_bond_restr	2.661
r_nbtor_refined	0.296
r_symmetry_hbond_refined	0.27
r_nbd_refined	0.206
r_xyhbond_nbd_refined	0.203
r_chiral_restr	0.149
r_symmetry_vdw_refined	0.127
r_gen_planes_refined	0.021
r_bond_refined_d	0.018

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	830
Solvent Atoms	194
Heterogen Atoms	16

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling