1XWI | pdb_00001xwi

Crystal Structure of VPS4B

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5	300	Ammonium Sulfate, HEPES, NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K, pH 7.50

Crystal Properties
Matthews coefficient	Solvent content
2.5	51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.058	α = 90
b = 88.058	β = 90
c = 112.574	γ = 120

Symmetry
Space Group	P 65

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		2003-01-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1		ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.8	76.6	99.3	0.058	0.058	9.7	10.9		12140			47.85

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.8	2.87	99.3		0.285	0.285	2.6

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	NONE	2.8	76.7	10917	10917	1190	98.8	0.199	0.192	0.19	0.26	0.26	RANDOM	47.85

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	0.5		1		-1.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.002
r_dihedral_angle_3_deg	20.641
r_dihedral_angle_4_deg	16.405
r_dihedral_angle_1_deg	6.41
r_scangle_it	3.804
r_scbond_it	2.294
r_angle_refined_deg	1.723
r_mcangle_it	1.686
r_mcbond_it	0.987
r_nbtor_refined	0.325
r_symmetry_vdw_refined	0.244
r_nbd_refined	0.242
r_xyhbond_nbd_refined	0.195
r_symmetry_hbond_refined	0.173
r_chiral_restr	0.11
r_bond_refined_d	0.018
r_gen_planes_refined	0.006
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	2508
Nucleic Acid Atoms
Solvent Atoms	9
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
SOLVE	phasing