2D3D

crystal structure of the RNA binding SAM domain of saccharomyces cerevisiae Vts1

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	PEG 4000, ammonium chloride, calcium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.9	38.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 27.38	α = 90
b = 27.89	β = 90
c = 99.91	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	IMAGE PLATE	RIGAKU RAXIS IV		2004-07-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-002	1.54

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	1.6	26.6	92.4	0.038	26.7	5.1	10544	9742	3

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)
	1.6	1.66	95.9		0.184	5.3	4	960

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	SIRAS	THROUGHOUT	1.6	26.6	3	13063	9721	471	92.35	0.20811	0.20811	0.20575	0.25571	RANDOM	14.955

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]
-0.2			-0.2		0.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.668
r_dihedral_angle_3_deg	11.903
r_dihedral_angle_4_deg	10.44
r_sphericity_free	5.706
r_dihedral_angle_1_deg	4.779
r_sphericity_bonded	4.587
r_scangle_it	3.739
r_scbond_it	3.555
r_rigid_bond_restr	3.269
r_mcangle_it	1.582
r_angle_refined_deg	1.334
r_mcbond_it	1.088
r_nbtor_refined	0.314
r_nbd_refined	0.209
r_symmetry_hbond_refined	0.154
r_symmetry_vdw_refined	0.133
r_xyhbond_nbd_refined	0.112
r_chiral_restr	0.087
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	681
Nucleic Acid Atoms
Solvent Atoms	73
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling
SHARP	phasing