4UZB | pdb_00004uzb

KSHV LANA (ORF73) C-terminal domain mutant bound to LBS1 DNA (R1039Q, R1040Q, K1055E, K1109A, D1110A, A1121E, K1138S, K1140D, K1141D)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2YPY	PDB ENTRY 2YPY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.6	297	0.9 UL OF 1.60 MM LANA(1008-1146) MUTANT, 0.96 MM DSDNA, 10 MM BISTRIS PH 6.5, 0.9 M NACL, AND 5 MM DTT WERE ADDED TO 0.9 UL OF RESERVOIR SOLUTION CONTAINING 50 MM MES PH 6.6, 27% PEG4000, AND 0.3 M AMMONIUM ACETATE IN A HANGING DROP SETUP. CRYSTALS GREW WITHIN FIVE DAYS AT 24 DEGREES CENTIGRADE.

Crystal Properties
Matthews coefficient	Solvent content
5.33	79.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 177.84	α = 90
b = 177.84	β = 90
c = 177.84	γ = 90

Symmetry
Space Group	I 21 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	PIXEL	DECTRIS PILATUS 6M	MIRRORS	2013-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11		PETRA III, DESY	P11

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	2.87	47.53	99.9	0.08	15.65	6.4		21605		2	79.32

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	2.87	3.04	99.7		0.86	1.99	6.3

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 ENTRY 2YPY	2.865	47.53	1.36	21618	1074	99.93	0.1234	0.1218	0.12	0.1547	0.16	96.5

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	22.735
f_angle_d	1.059
f_chiral_restr	0.043
f_bond_d	0.008
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2188
Nucleic Acid Atoms	814
Solvent Atoms	105
Heterogen Atoms

Software

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