Experiment: 7JOD

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4K8Y	4k8y, 6DWF
experimental model	PDB	6DWF	4k8y, 6DWF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	2.4M Ammonium Sulfate, 2%PEG400, 10mM CdCl2

Crystal Properties
Matthews coefficient	Solvent content
3.24	62.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.185	α = 90
b = 104.185	β = 90
c = 87.013	γ = 120

Symmetry
Space Group	P 31 2 1

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		2018-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.000	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	1.33	50	96.8	0.073	18.2	5		120718

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.33	1.35	65.6		0.798		2.6

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	4k8y, 6DWF	1.33	39	105106	1099	85.84	0.114	0.1138	0.114	0.1325	0.1331	RANDOM	18.849

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]
-0.65	-0.33		-0.65		2.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.319
r_dihedral_angle_4_deg	22.946
r_dihedral_angle_3_deg	13.762
r_dihedral_angle_1_deg	7.141
r_rigid_bond_restr	5.28
r_angle_refined_deg	1.953
r_angle_other_deg	1.632
r_chiral_restr	0.112
r_bond_refined_d	0.013
r_gen_planes_refined	0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.319
r_dihedral_angle_4_deg	22.946
r_dihedral_angle_3_deg	13.762
r_dihedral_angle_1_deg	7.141
r_rigid_bond_restr	5.28
r_angle_refined_deg	1.953
r_angle_other_deg	1.632
r_chiral_restr	0.112
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2951
Nucleic Acid Atoms
Solvent Atoms	627
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	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.