Experiment: 8H2X

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	PEG 3350, Sodium bromide

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.866	α = 90
b = 101.866	β = 90
c = 101.655	γ = 120

Symmetry
Space Group	P 3 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	RIGAKU HyPix-6000HE		2022-06-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-X	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.69	50	99.9	0.982	16.6	14.1		17359

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.69	2.79			0.903

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	Alphafold2 model	2.69	33.37	15609	845	94.5	0.2499	0.2488	0.27	RANDOM	49.828

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]
0.22	0.11		0.22		-0.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.725
r_dihedral_angle_1_deg	6.059
r_mcangle_it	5.773
r_dihedral_angle_2_deg	5.43
r_mcbond_it	3.93
r_mcbond_other	3.93
r_angle_refined_deg	1.59
r_angle_other_deg	0.696
r_chiral_restr	0.069
r_bond_other_d	0.028

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.725
r_dihedral_angle_1_deg	6.059
r_mcangle_it	5.773
r_dihedral_angle_2_deg	5.43
r_mcbond_it	3.93
r_mcbond_other	3.93
r_angle_refined_deg	1.59
r_angle_other_deg	0.696
r_chiral_restr	0.069
r_bond_other_d	0.028
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4302
Nucleic Acid Atoms
Solvent Atoms	85
Heterogen Atoms	62

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	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 R01GM133198.