Experiment: 5XA4

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	6	293	50mM MES (pH6.0), 50mM KPi buffer (pH7.0), 500mM Potassium sodium tartrate

Crystal Properties
Matthews coefficient	Solvent content
3.32	62.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 154.002	α = 90
b = 154.002	β = 90
c = 36.626	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	1.3	50	99.5	0.043	0.046	0.015	14.8	8.7		122191

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	1.3	1.35	96.9		0.303	0.332	0.133	0.926		5.8	11785

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	1.3	19.05	115462	6109	99.06	0.169	0.1683	0.1829	RANDOM	15.876

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	34.441
r_dihedral_angle_4_deg	19.541
r_dihedral_angle_3_deg	9.728
r_dihedral_angle_1_deg	6.084
r_angle_refined_deg	1.618
r_angle_other_deg	0.885
r_chiral_restr	0.073
r_bond_refined_d	0.008
r_bond_other_d	0.006
r_gen_planes_refined	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.441
r_dihedral_angle_4_deg	19.541
r_dihedral_angle_3_deg	9.728
r_dihedral_angle_1_deg	6.084
r_angle_refined_deg	1.618
r_angle_other_deg	0.885
r_chiral_restr	0.073
r_bond_refined_d	0.008
r_bond_other_d	0.006
r_gen_planes_refined	0.005
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2670
Nucleic Acid Atoms
Solvent Atoms	481
Heterogen Atoms	80

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.