Experiment: 7CY8

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7CY4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	290	15% (v/v) 2-propanol, 0.1 M sodium citrate, pH 5.0, and 10% (w/v) PEG 10000

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 154.488	α = 90
b = 125.646	β = 102.96
c = 64.058	γ = 90

Symmetry
Space Group	C 1 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	173	PIXEL	DECTRIS PILATUS3 S 6M		2020-05-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NFPSS BEAMLINE BL18U	0.9791	NFPSS	BL18U

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	2.4	49.28	94.6	0.088	1	13.1	4.7		35155

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	2.4	2.5			1.02	0.53	1.6

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7CY4	2.4	49.28	33382	1757	75.42	0.1923	0.19	0.2351	RANDOM	49.153

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]
0.37		-1.51	-1.24		1.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.124
r_sphericity_free	22.417
r_sphericity_bonded	21.47
r_dihedral_angle_4_deg	20.581
r_dihedral_angle_3_deg	15.312
r_dihedral_angle_1_deg	5.525
r_rigid_bond_restr	4.36
r_angle_other_deg	2.869
r_angle_refined_deg	1.281
r_chiral_restr	0.066

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.124
r_sphericity_free	22.417
r_sphericity_bonded	21.47
r_dihedral_angle_4_deg	20.581
r_dihedral_angle_3_deg	15.312
r_dihedral_angle_1_deg	5.525
r_rigid_bond_restr	4.36
r_angle_other_deg	2.869
r_angle_refined_deg	1.281
r_chiral_restr	0.066
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6366
Nucleic Acid Atoms	352
Solvent Atoms	198
Heterogen Atoms	25

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	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.