Experiment: 6U1Q

Crystal Structure of VpsO (VC0937) Kinase domain

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4JLV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	0.2 M sodium thiocyanate, pH 6.9, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.63	66.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 171.43	α = 90
b = 171.43	β = 90
c = 44.39	γ = 120

Symmetry
Space Group	P 64

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2018-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1	APS	23-ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	2.87	44.39	100	0.096	0.99	9.2	4.6		17506

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.87	3.03			0.66	0.73	2.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4JLV	2.87	42.858	16990	810	97.09	0.1775	0.1749	0.1797	0.2283	0.2276	74.2976

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3121
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	34

Software

Software
Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing