Experiment: 2YPY

KSHV LANA (ORF73) C-terminal domain, decameric ring: monoclinic crystal form

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	285	1.5 UL OF 2.0 MM PROTEIN IN 5 MM BISTRIS, PH 6.5, 10 MM DTT WERE ADDED TO 1.5 UL OF 0.1 M SODIUM BICINE, PH 9.0, 1.0 M LITHIUM CHLORIDE, 7 % (W/V) PEG 6000. THE MIXTURE WAS INCUBATED AT 12 DEGREES CENTIGRADE IN A HANGING DROP SETUP. CRYSTALS GREW IN A FEW DAYS AND WERE CRYO-PROTECTED BY SHORT SOAKING IN 0.1 M SODIUM BICINE, PH 9.0, 1.0 M LITHIUM CHLORIDE, 7 % (W/V) PEG 6000, 25 % (V/V) GLYCEROL.

Crystal Properties
Matthews coefficient	Solvent content
2.81	56.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.74	α = 90
b = 175.92	β = 95.5
c = 97.58	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	MARRESEARCH	MIRRORS	2012-06-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	1.07208, 0.97974	BESSY	14.2

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	2.45	20	85.7	0.05	16.24	3.8		54311		2	51.04

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	2.45	2.53	21.7		0.48	2.6	3.6

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	SAD	NONE	2.453	19.652	1.99	54308	2762	85.89	0.2224	0.2207	0.2145	0.2522	0.2471	71.9

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]
0.3303		-1.5344	2.0336		-2.4059

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	10.115
f_angle_d	0.645
f_chiral_restr	0.045
f_plane_restr	0.004
f_bond_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10819
Nucleic Acid Atoms
Solvent Atoms	149
Heterogen Atoms	24

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing