2QP9

Crystal Structure of S.cerevisiae Vps4

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	293	Sodium Acetate, CdSO4, pH 6.5, temperature 293K, VAPOR DIFFUSION

Crystal Properties
Matthews coefficient	Solvent content
3.29	62.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.553	α = 90
b = 86.553	β = 90
c = 236.061	γ = 120

Symmetry
Space Group	P 65 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		CCD				M	SINGLE WAVELENGTH
2	1	x-ray		CCD				M	MAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D		APS	23-ID-D
2	SYNCHROTRON	APS BEAMLINE 23-ID-D		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	2.9	50	98.1	0.063	37.5	13.2		12599

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	2.9	3	99.2		0.606	3.8

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	2.9	10	10792	576	95.1	0.25996	0.25842	0.28819	RANDOM	58.579

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]
2.69	1.34		2.69		-4.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.004
r_dihedral_angle_3_deg	21.48
r_dihedral_angle_4_deg	20.824
r_dihedral_angle_1_deg	5.045
r_scangle_it	1.645
r_angle_refined_deg	1.137
r_scbond_it	1.052
r_mcangle_it	0.945
r_mcbond_it	0.515
r_symmetry_vdw_refined	0.372
r_nbtor_refined	0.303
r_nbd_refined	0.214
r_metal_ion_refined	0.2
r_symmetry_hbond_refined	0.131
r_xyhbond_nbd_refined	0.105
r_symmetry_metal_ion_refined	0.073
r_chiral_restr	0.071
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
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_other
r_symmetry_vdw_other
r_symmetry_hbond_other
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	2067
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	7

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction