Experiment: 6EF5

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QJB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	277.15	0.1 M Tris pH 8.5, 0.1 M MgCl2, 0.001 M NiCl2 and 22% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.691	α = 90
b = 94.691	β = 90
c = 234.43	γ = 120

Symmetry
Space Group	P 65

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		2018-04-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.95365	Australian Synchrotron	MX2

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	2.44	82	100	0.222	0.232	0.068	0.996	7.7	11.6		44169

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	2.44	2.53	100		1.036	1.083	0.315	0.397		11.8

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	1QJB	2.44	82	41980	2108	99.98	0.1947	0.1922	0.19	0.2438	0.24	RANDOM	49.913

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]
-21.3			-21.3		42.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.717
r_dihedral_angle_3_deg	19.122
r_dihedral_angle_4_deg	14.976
r_dihedral_angle_1_deg	6.008
r_angle_refined_deg	1.797
r_angle_other_deg	1.029
r_chiral_restr	0.096
r_bond_refined_d	0.018
r_gen_planes_refined	0.008
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.717
r_dihedral_angle_3_deg	19.122
r_dihedral_angle_4_deg	14.976
r_dihedral_angle_1_deg	6.008
r_angle_refined_deg	1.797
r_angle_other_deg	1.029
r_chiral_restr	0.096
r_bond_refined_d	0.018
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7335
Nucleic Acid Atoms
Solvent Atoms	14
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
xia2	data reduction
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.