353D | pdb_0000353d

CRYSTAL STRUCTURE OF DOMAIN A OF THERMUS FLAVUS 5S RRNA AND THE CONTRIBUTION OF WATER MOLECULES TO ITS STRUCTURE

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RNA	NDB ENTRY ARN035 (PDB ENTRY 1RNA)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.6	51.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.1	α = 90
b = 30.1	β = 90
c = 86.8	γ = 90

Symmetry
Space Group	P 43

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	153	IMAGE PLATE	MARRESEARCH			M
2	1	x-ray	153	IMAGE PLATE	MARRESEARCH			M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	CONVENTIONAL Mo	0.7107
2	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.9200	EMBL/DESY, HAMBURG	X11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.4		83.5				2477

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-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION		NDB ENTRY ARN035 (PDB ENTRY 1RNA)	2.4	8	2477			0.18			23.9

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]

RMS Deviations
Key	Refinement Restraint Deviation
n_angle_d	0.068
n_chiral_restr	0.036
n_bond_d	0.025
n_planar_d	0.014
n_hb_or_metal_coord
n_sugar_bond_it
n_sugar_angle_it
n_phos_bond_it
n_phos_angle_it
n_bond_angle_restr
n_dihedral_angle_restr
n_impr_tor
n_sugar_bond_d
n_sugar_bond_angle_d
n_phos_bond_d
n_phos_bond_angle_d
n_plane_restr
n_singtor_nbd
n_multtor_nbd
n_xhyhbond_nbd

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	508
Solvent Atoms	158
Heterogen Atoms

Software

Software
Software Name	Purpose
AMoRE	phasing
NUCLSQ	refinement
XDS	data reduction
DENZO	data reduction