Experiment: 10CX

Crystal structure of Pyrobaculum calidifontis Rpp30

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	The best diffracting crystals were grown by vapor diffusion equilibrated with 100 mM Tris-bicine, pH 8.5, 10% (w/v) PEG 20,000, 20% (v/v) PEG MME 550, 30 mM sodium nitrate, 30 mM disodium hydrogen phosphate, 30 mM ammonium sulfate. Crystals were sufficiently cryo-protected by the crystallization solution containing 20% (v/v) PEG MME 550 without further supplementation prior to flash freezing with liquid nitrogen.

Crystal Properties
Matthews coefficient	Solvent content
2	38.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.228	α = 90
b = 53.898	β = 105.69
c = 42.213	γ = 90

Symmetry
Space Group	P 1 21 1

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	2013-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.77484	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	0.897	40.64	83.8	0.059	0.065	0.998	13.8	5.3		97752			8.66

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	0.897	0.953	25.3		1.036	1.151	0.541	1.6	1.6

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	0.9	34.88	1.34	97748	4987	83.78	0.1362	0.1351	0.1352	0.1572	0.1571	14.21

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	13.7764
f_angle_d	1.2311
f_chiral_restr	0.0996
f_plane_restr	0.0118
f_bond_d	0.0112

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1402
Nucleic Acid Atoms
Solvent Atoms	208
Heterogen Atoms	56

Software

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