3BW1

Crystal structure of homomeric yeast Lsm3 exhibiting novel octameric ring organisation

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	1.75M lithium sulfate, 8% (v/v) 2-methyl-2,4-pentanediol, 0.1M imidazole (pH 7.0), 10mM uridine-5-monophosphate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.743	α = 90
b = 83.743	β = 90
c = 141.931	γ = 90

Symmetry
Space Group	I 4 2 2

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	MARMOSAIC 300 mm CCD		2005-11-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.9793	APS	23-ID-D

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	2.45	36.25	97.6	0.086	23.7		9583	9073	2	2	71.8

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	2.45	2.57	83.9		1.405	1.5

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1I81	2.5	24.04	9073	8603	429	99.55	0.21694	0.21694	0.21564	0.24296	RANDOM	74.78

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
r_dihedral_angle_2_deg	34.878
r_dihedral_angle_3_deg	20.438
r_dihedral_angle_4_deg	17.688
r_dihedral_angle_1_deg	7.503
r_scangle_it	3.416
r_scbond_it	2.276
r_angle_refined_deg	2.125
r_mcangle_it	1.392
r_mcbond_it	0.798
r_nbtor_refined	0.324

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.878
r_dihedral_angle_3_deg	20.438
r_dihedral_angle_4_deg	17.688
r_dihedral_angle_1_deg	7.503
r_scangle_it	3.416
r_scbond_it	2.276
r_angle_refined_deg	2.125
r_mcangle_it	1.392
r_mcbond_it	0.798
r_nbtor_refined	0.324
r_symmetry_vdw_refined	0.308
r_nbd_refined	0.254
r_symmetry_hbond_refined	0.221
r_chiral_restr	0.129
r_xyhbond_nbd_refined	0.127
r_bond_refined_d	0.021
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1368
Nucleic Acid Atoms
Solvent Atoms	2
Heterogen Atoms	37

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.