2G3K

Crystal structure of the C-terminal domain of Vps28

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	293	1 M AS 100 mM sodium acetate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.84	67.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.579	α = 90
b = 117.579	β = 90
c = 294.116	γ = 120

Symmetry
Space Group	P 61 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	MARRESEARCH	Collimating mirror+channel cut Si(111) monochromator + focussing toroidal mirror.	2004-10-10	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 4	diamond monochromator-germanium 220 vertically foucssing mirror - horizontally focussing multilayer mirror.	2005-01-01	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.97797	ESRF	BM14
2	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.933	ESRF	ID14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.05	20	99.5			24827	23615	3	3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	3.05	3.21	99.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	3.05	19.94	23684	22301	1205	99.25	0.21599	0.21599	0.21299	0.27269	RANDOM	73.974

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]
-0.11	-0.05		-0.11		0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.328
r_dihedral_angle_3_deg	23.397
r_dihedral_angle_4_deg	19.324
r_dihedral_angle_1_deg	5.998
r_scangle_it	2.729
r_angle_refined_deg	1.749
r_scbond_it	1.674
r_mcangle_it	1.069
r_mcbond_it	0.727
r_symmetry_hbond_refined	0.345

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.328
r_dihedral_angle_3_deg	23.397
r_dihedral_angle_4_deg	19.324
r_dihedral_angle_1_deg	5.998
r_scangle_it	2.729
r_angle_refined_deg	1.749
r_scbond_it	1.674
r_mcangle_it	1.069
r_mcbond_it	0.727
r_symmetry_hbond_refined	0.345
r_nbtor_refined	0.326
r_nbd_refined	0.258
r_symmetry_vdw_refined	0.243
r_xyhbond_nbd_refined	0.197
r_chiral_restr	0.126
r_bond_refined_d	0.016
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5390
Nucleic Acid Atoms
Solvent Atoms	56
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHELXS	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 R01GM157729.