Experiment: 7X6H

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M Magnesium chloride hexahydrate, 0.1 M Tris pH 7.5, 13 % w/v PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.087	α = 90
b = 123.808	β = 90
c = 150.157	γ = 90

Symmetry
Space Group	P 21 21 21

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 EIGER X 16M		2021-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.900	SPring-8	BL44XU

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	2.6	47.76	99.9	0.11	0.12	0.047	0.997	10.9	6.6		25039

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	2.6	2.72	100		1.317	1.425	0.539	0.749	1.7	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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	AlphaFold structure	2.6	35.903	24975	1231	99.816	0.247	0.2448	0.2954	81.29

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]
5.221			-1.351		-3.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.778
r_dihedral_angle_3_deg	17.401
r_dihedral_angle_4_deg	15.738
r_lrange_it	8.015
r_dihedral_angle_1_deg	4.353
r_scangle_it	4.334
r_mcangle_it	3.872
r_scbond_it	2.589
r_mcbond_it	2.273
r_angle_refined_deg	0.711

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.778
r_dihedral_angle_3_deg	17.401
r_dihedral_angle_4_deg	15.738
r_lrange_it	8.015
r_dihedral_angle_1_deg	4.353
r_scangle_it	4.334
r_mcangle_it	3.872
r_scbond_it	2.589
r_mcbond_it	2.273
r_angle_refined_deg	0.711
r_nbtor_refined	0.288
r_nbd_refined	0.181
r_symmetry_nbd_refined	0.149
r_xyhbond_nbd_refined	0.108
r_symmetry_xyhbond_nbd_refined	0.075
r_chiral_restr	0.063
r_bond_refined_d	0.002
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4937
Nucleic Acid Atoms
Solvent Atoms	43
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
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 R01GM133198.