1L3D | pdb_00001l3d

Low Resolution Crystal Structure of a Viral RNA Pseudoknot

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	437D	PDB entry 437D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	277	ammonium sulfate, sodium citrate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K

Crystal Properties
Matthews coefficient	Solvent content
5.65	78.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.81	α = 90
b = 107.81	β = 90
c = 107.81	γ = 90

Symmetry
Space Group	I 21 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	IMAGE PLATE	MARRESEARCH	mirrors	1997-06-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL1-5	1.0800	SSRL	BL1-5

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	2.85	30	100	0.054	39.5	9.2	5034	5034		-3	63.1

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)
	2.85	2.95	100		0.286	9.3	8.9	486

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-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 437D	2.85	20	4989	4989	514	99.7	0.271	0.2683	0.275	0.2804	RANDOM	43.3

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]
1.768			1.768		1.768

RMS Deviations
Key	Refinement Restraint Deviation
c_angle_deg	1
c_bond_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	677
Solvent Atoms	14
Heterogen Atoms

Software

Software
Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling