Experiment: 5K3V

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NV2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	0.05 M MES.OH pH 6.5, 0.7 M ammonium sulfate, 5% 1,4-dioxane, 0.01 M Tris.HCl pH 7.0, 0.1 M potassium chloride, and 0.005 M dithiothreitol

Crystal Properties
Matthews coefficient	Solvent content
2.98	58.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 178.22	α = 90
b = 178.22	β = 90
c = 116.43	γ = 120

Symmetry
Space Group	H 3

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 EIGER X 16M		2015-05-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.97858	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.461	92.949	98.8	0.14	4.4	4.3		236195

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	1.461	1.54	97.8		4.691	0.2	3.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2NV2	1.9	92.949	101932	5406	98.76	0.178	0.1767	0.19	0.2033	0.18	RANDOM	31.379

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]
-1.18	-0.59		-1.18		3.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.034
r_dihedral_angle_4_deg	15.523
r_dihedral_angle_3_deg	13.498
r_dihedral_angle_1_deg	6.027
r_mcangle_it	3.716
r_mcbond_it	2.611
r_mcbond_other	2.609
r_angle_refined_deg	1.723
r_angle_other_deg	1.39
r_chiral_restr	0.103

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.034
r_dihedral_angle_4_deg	15.523
r_dihedral_angle_3_deg	13.498
r_dihedral_angle_1_deg	6.027
r_mcangle_it	3.716
r_mcbond_it	2.611
r_mcbond_other	2.609
r_angle_refined_deg	1.723
r_angle_other_deg	1.39
r_chiral_restr	0.103
r_bond_refined_d	0.015
r_gen_planes_refined	0.009
r_bond_other_d	0.007
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8222
Nucleic Acid Atoms
Solvent Atoms	501
Heterogen Atoms	57

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.