6P22 | pdb_00006p22

Photorhabdus Virulence Cassette (PVC) PAAR repeat protein Pvc10 in complex with a T4 gp5 beta-helix fragment modified to mimic Pvc8, the central spike protein of PVC

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4JJ2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	MPD 28-34% PEG 2000 8-18% 100 mM Imidazole pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.305	α = 90
b = 56.963	β = 90
c = 222.994	γ = 90

Symmetry
Space Group	P 21 21 21

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	DYNAMICALLY BENDABLE MIRROR	2013-08-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0000	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	2.29	50	99.2	0.125	0.998	9.78	6.2		37669			45.19

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.29	2.43	96		0.702	0.95	2.05

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation 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	FREE R-VALUE	4JJ2	2.291	45.213	1.93	37478	1891	98.88	0.184	0.1819	0.1844	0.2224	0.2209	49.2

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	11.186
f_angle_d	0.483
f_chiral_restr	0.051
f_plane_restr	0.003
f_bond_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3084
Nucleic Acid Atoms
Solvent Atoms	141
Heterogen Atoms	59

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
X-GEN	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.