Experiment: 7C4D

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BF8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	289	20% PEG 8000, 50mM Li2SO4, 50mM Na2SO4, MES pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67	α = 90
b = 67	β = 90
c = 62	γ = 120

Symmetry
Space Group	P 32

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 PILATUS3 6M		2018-06-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.97892	SSRF	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.03	58.024	99.7	0.097	0.997	9.5	7.5		20051			60.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.03	2.08	95.8		2.13	0.354		4.3

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3bf8	2.03	58.02	20015	1052	99.597	0.203	0.1999	0.2	0.2613	0.26	68.586

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]
-0.547	-0.273		-0.547		1.773

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.271
r_dihedral_angle_4_deg	22.927
r_dihedral_angle_3_deg	18.413
r_lrange_it	13.206
r_scangle_it	9.295
r_mcangle_it	7.387
r_scbond_it	6.542
r_dihedral_angle_1_deg	5.828
r_mcbond_it	5.358
r_angle_refined_deg	1.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.271
r_dihedral_angle_4_deg	22.927
r_dihedral_angle_3_deg	18.413
r_lrange_it	13.206
r_scangle_it	9.295
r_mcangle_it	7.387
r_scbond_it	6.542
r_dihedral_angle_1_deg	5.828
r_mcbond_it	5.358
r_angle_refined_deg	1.43
r_nbtor_refined	0.308
r_symmetry_xyhbond_nbd_refined	0.249
r_symmetry_nbd_refined	0.204
r_nbd_refined	0.198
r_xyhbond_nbd_refined	0.135
r_chiral_restr	0.113
r_gen_planes_refined	0.008
r_bond_refined_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2088
Nucleic Acid Atoms
Solvent Atoms	66
Heterogen Atoms	17

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MoRDa	phasing
Coot	model building
DMMulti	model building
MOLREP	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.