Experiment: 10CY

Crystal structure of Pyrobaculum islandicum Rpp30/Pop5 complex

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		T. neutrophilus Rpp30

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	303	Crystals were grown from 1-2 mg/ml protein stock solutions at 303 K by vapor diffusion over a narrow range of equilibration solutions optimized around 100 mM Tris-HCl, pH 8.5, 200 mM KCl, 20% (v/v) ethanol. Crystals were cryo-protected by supplementing the crystallization solutions with 25% glycerol (v/v) and subsequently flash frozen with liquid nitrogen.

Crystal Properties
Matthews coefficient	Solvent content
3.33	63.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.217	α = 90
b = 108.217	β = 90
c = 139.169	γ = 90

Symmetry
Space Group	P 41 21 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	RAYONIX MX-300	Mirrors	2016-03-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.1051	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.49	48.4	91.2	0.131	0.142	0.996	11.7	7.5		27135			50.93

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.49	2.6	37.2		1.32	1.44	0.632	1.5	6.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.49	48.4	1.34	27128	1354	91.2	0.2015	0.1992	0.1991	0.244	0.2434	54.58

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	18.2482
f_angle_d	0.8353
f_chiral_restr	0.0504
f_plane_restr	0.0085
f_bond_d	0.0056

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4113
Nucleic Acid Atoms
Solvent Atoms	44
Heterogen Atoms	2

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing