Experiment: 7MJD

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3N80

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	289	PEG 4000, glycerol, tris-bicine, ethyleneglycols

Crystal Properties
Matthews coefficient	Solvent content
2.49	51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.04	α = 90
b = 102.04	β = 90
c = 186.037	γ = 120

Symmetry
Space Group	P 32 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 PILATUS 6M	Rh coated collimating mirrors, K-B focusing mirrors	2018-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.97946	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.12	88.369	99.9	0.081	0.088	0.034	11.4	6.7	64238	64238

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.12	2.23	100		0.793	0.793	0.859	0.327	1	6.9

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	3N80	2.12	30.37	60846	3298	99.74	0.1825	0.1805	0.19	0.2188	0.23	RANDOM	48.122

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]
0.79	0.4		0.79		-2.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.516
r_dihedral_angle_4_deg	17.335
r_dihedral_angle_3_deg	16.281
r_dihedral_angle_1_deg	6.618
r_angle_refined_deg	1.535
r_angle_other_deg	0.965
r_chiral_restr	0.096
r_bond_refined_d	0.011
r_bond_other_d	0.006
r_gen_planes_refined	0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.516
r_dihedral_angle_4_deg	17.335
r_dihedral_angle_3_deg	16.281
r_dihedral_angle_1_deg	6.618
r_angle_refined_deg	1.535
r_angle_other_deg	0.965
r_chiral_restr	0.096
r_bond_refined_d	0.011
r_bond_other_d	0.006
r_gen_planes_refined	0.006
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7704
Nucleic Acid Atoms
Solvent Atoms	186
Heterogen Atoms	240

Software

Software
Software Name	Purpose
XDS	data reduction
SCALA	data scaling
PHASER	phasing
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.