Experiment: 6EJV

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6EJS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.12 M 1,6-Hexanediol 0.12 M 1-Butanol 0.12 M 1,2-Propanediol 0.12 M 2-Propanol 0.12 M 1,4-Butanediol 0.12 M 1,3-Propanediol 0.1 M Tris and Bicine pH 8.5 12.5 % v/v 2-Methyl- -2,4,-pentanediol 12.5 % PEG 1000 12.5 % w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.44	α = 90
b = 58.47	β = 90
c = 72.45	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	PIXEL	Bruker PHOTON II	HELIOS MX	2017-05-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	LIQUID ANODE	Excillum MetalJet D2+ 70 kV	1.3418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.75	45.5	99.9	0.09	0.101	0.045	0.998	17.9	9.1		24852		-3	14.48

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	1.75	1.78	100		0.872	1.018	0.518	0.78	1.8	7.1

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	6EJS	1.75	45.5	24802	1199	99.83	0.1574	0.1569	0.17	0.1667	0.18	RANDOM	22.3148

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]
-1.04			-0.42		1.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.125
r_dihedral_angle_3_deg	13.367
r_dihedral_angle_4_deg	13.255
r_dihedral_angle_1_deg	5.696
r_angle_other_deg	3.691
r_mcangle_it	2.527
r_angle_refined_deg	1.818
r_mcbond_it	1.73
r_mcbond_other	1.719
r_chiral_restr	0.114

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.125
r_dihedral_angle_3_deg	13.367
r_dihedral_angle_4_deg	13.255
r_dihedral_angle_1_deg	5.696
r_angle_other_deg	3.691
r_mcangle_it	2.527
r_angle_refined_deg	1.818
r_mcbond_it	1.73
r_mcbond_other	1.719
r_chiral_restr	0.114
r_bond_refined_d	0.019
r_gen_planes_other	0.014
r_gen_planes_refined	0.011
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1676
Nucleic Acid Atoms
Solvent Atoms	280
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	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.