Experiment: 7NY8

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4OBE	4OBE, 4N6T
experimental model	PDB	4N6T	4OBE, 4N6T

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	0.1M imidazole, 0.1M MES monohydrate, 20% w/v PEG 500 MME, 10% w/v PEG 20000, 0.12M 1,6-hexanediol, 0.12M 1,2-propanediol, 0.12M 1,4-butanediol, 0.12M 1-butanol, 0.12M 2-propanol, 0.12M 1,3-propanediol

Crystal Properties
Matthews coefficient	Solvent content
2.29	39.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.008	α = 90
b = 168.775	β = 92.7
c = 39.653	γ = 90

Symmetry
Space Group	P 1 21 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 EIGER2 X 16M		2020-10-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.8	168.77	100	0.072	0.078	0.03	0.999	19.3	6.9		47236			25.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.83	100		0.734	0.794	0.3	0.821		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	4OBE, 4N6T	1.8	84.53	44810	2378	100	0.1568	0.154	0.17	0.2097	0.22	RANDOM	29.893

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]
1.03		-0.05	-1.21		0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.552
r_dihedral_angle_4_deg	19.798
r_dihedral_angle_3_deg	12.334
r_dihedral_angle_1_deg	6.574
r_angle_refined_deg	1.314
r_rigid_bond_restr	1.304
r_angle_other_deg	1.223
r_chiral_restr	0.052
r_bond_refined_d	0.005
r_gen_planes_refined	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.552
r_dihedral_angle_4_deg	19.798
r_dihedral_angle_3_deg	12.334
r_dihedral_angle_1_deg	6.574
r_angle_refined_deg	1.314
r_rigid_bond_restr	1.304
r_angle_other_deg	1.223
r_chiral_restr	0.052
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4253
Nucleic Acid Atoms
Solvent Atoms	258
Heterogen Atoms	58

Software

Software
Software Name	Purpose
DIALS	data scaling
PHASER	phasing
REFMAC	refinement
DIALS	data reduction

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.