3ETU

Crystal structure of yeast Dsl1p

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	298	0.1 M HEPES, pH 7.5, 0.45-0.50 M sodium citrate, VAPOR DIFFUSION, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
3.24	62.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.62	α = 90
b = 110.62	β = 90
c = 77.203	γ = 120

Symmetry
Space Group	P 32 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	ADSC QUANTUM 315		2007-10-28	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 315		2007-10-15	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.1000	NSLS	X25
2	SYNCHROTRON	NSLS BEAMLINE X25	0.9795, 0.9797, 0.9641	NSLS	X25

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
1,2	2.4	100	99.2	0.073	28.7	7.1		21447

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)
	2.4	2.49	96.8		0.433	2.8	6.6	2056

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.4	40	20321	1103	99.13	0.23082	0.22892	0.26607	RANDOM	69.084

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]
-4.97	-2.49		-4.97		7.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.348
r_dihedral_angle_4_deg	18.374
r_dihedral_angle_3_deg	15.458
r_dihedral_angle_1_deg	5.697
r_mcangle_it	4.301
r_scangle_it	3.967
r_scbond_it	2.931
r_mcbond_it	2.876
r_angle_refined_deg	1.126
r_nbtor_refined	0.304
r_nbd_refined	0.204
r_symmetry_vdw_refined	0.185
r_xyhbond_nbd_refined	0.144
r_symmetry_hbond_refined	0.142
r_chiral_restr	0.074
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2549
Nucleic Acid Atoms
Solvent Atoms	49
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data collection
SHARP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling