4ADQ | pdb_00004adq

CRYSTAL STRUCTURE OF THE MOUSE COLONY-STIMULATING FACTOR 1 (MCSF-1) CYTOKINE IN COMPLEX WITH THE VIRAL RECEPTOR BARF1

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2CH8	PDB ENTRIES 2CH8 AND 3UF5
experimental model	PDB	3UF5	PDB ENTRIES 2CH8 AND 3UF5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8		pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
3.38	61.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 234.75	α = 90
b = 234.75	β = 90
c = 96.04	γ = 120

Symmetry
Space Group	H 3

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	MIRRORS	2011-05-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29		ESRF	ID29

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	4.5	40	94.5	0.15	5.7	1.7		11082		2	138.7

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	4.5	4.62	93.2		0.68	1.6	1.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	PDB ENTRIES 2CH8 AND 3UF5	4.5	117.375	1.96	11078	1112	94.46	0.2265	0.2226	0.25	0.2622	0.28	187.44

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]
-22.3592			-22.3592		44.7184

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.924
f_angle_d	0.713
f_chiral_restr	0.041
f_bond_d	0.003
f_plane_restr	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10591
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	167

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	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.