Experiment: 6WFI

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JC5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	50 mM sodium chloride, 100 mM Bis-Tris:HCl pH 7.0, 2.6 M ammonium sulfate, 5% PEG 400

Crystal Properties
Matthews coefficient	Solvent content
1.86	34.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.837	α = 90
b = 68.837	β = 90
c = 103.37	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	CCD	RAYONIX MX300HE	MD2 Micro Diffractometer	2017-02-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.37	30	99.8	0.059	0.059	0.061	0.016	14.2	14.2		52867		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.37	1.42	100		0.47	0.47	6.516	13.3

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	1JC5	1.37	25.86	50250	2548	99.74	0.1486	0.1474	0.1736	RANDOM	19.115

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]
0.19			0.19		-0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.574
r_dihedral_angle_4_deg	13.827
r_dihedral_angle_3_deg	12.545
r_dihedral_angle_1_deg	7.452
r_angle_refined_deg	2.617
r_angle_other_deg	1.653
r_chiral_restr	0.287
r_bond_refined_d	0.021
r_gen_planes_refined	0.012
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.574
r_dihedral_angle_4_deg	13.827
r_dihedral_angle_3_deg	12.545
r_dihedral_angle_1_deg	7.452
r_angle_refined_deg	2.617
r_angle_other_deg	1.653
r_chiral_restr	0.287
r_bond_refined_d	0.021
r_gen_planes_refined	0.012
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1109
Nucleic Acid Atoms
Solvent Atoms	314
Heterogen Atoms	74

Software

Software
Software Name	Purpose
HKL-2000	data reduction
PHASER	phasing
SCALEPACK	data scaling
ARP/wARP	model building
Coot	model building
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.