Experiment: 5XIE

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3W8O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	50mM HEPES (pH7.5), 50mM KPi buffer (pH7.0), 0.63M ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
3.32	62.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 153.622	α = 90
b = 153.622	β = 90
c = 36.825	γ = 120

Symmetry
Space Group	P 61

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	MARMOSAIC 225 mm CCD		2015-09-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B2	1.000	SPring-8	BL26B2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.05	50	99.8	0.057	0.06	0.019	20	10.4		31662

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.12	100		0.114	0.12	0.038	0.995		9.8	3087

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3W8O	2.05	18.8	29932	1592	99.68	0.1742	0.1727	0.203	RANDOM	25.532

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
r_dihedral_angle_2_deg	35.787
r_dihedral_angle_4_deg	22.513
r_dihedral_angle_3_deg	11.274
r_dihedral_angle_1_deg	5.965
r_angle_refined_deg	1.477
r_angle_other_deg	0.897
r_chiral_restr	0.071
r_bond_refined_d	0.009
r_bond_other_d	0.007
r_gen_planes_refined	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.787
r_dihedral_angle_4_deg	22.513
r_dihedral_angle_3_deg	11.274
r_dihedral_angle_1_deg	5.965
r_angle_refined_deg	1.477
r_angle_other_deg	0.897
r_chiral_restr	0.071
r_bond_refined_d	0.009
r_bond_other_d	0.007
r_gen_planes_refined	0.005
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2664
Nucleic Acid Atoms
Solvent Atoms	214
Heterogen Atoms	78

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data collection
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
DENZO	data reduction
MOLREP	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.