Experiment: 8XTD

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6WZU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277.15	0.1 M Tris-HCl (pH 7.5-9.0), 1.4 M NaH2PO4, 2-15% Glycerol

Crystal Properties
Matthews coefficient	Solvent content
3.54	65.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.217	α = 90
b = 81.217	β = 90
c = 133.485	γ = 120

Symmetry
Space Group	P 32 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		2023-11-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim I (All)	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	2.7	23.09	99.8	0.06	10.7	4		16226

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.83	100		0.41	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.7	23	14471	684	99.717	0.224	0.2208	0.2207	0.2882	0.2882	45.378

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]
0.553	0.276		0.553		-1.794

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.644
r_lrange_it	14.067
r_dihedral_angle_6_deg	13.451
r_scangle_it	8.473
r_dihedral_angle_2_deg	7.581
r_dihedral_angle_1_deg	7.376
r_mcangle_it	6.566
r_scbond_it	5.511
r_mcbond_it	4.11
r_angle_refined_deg	1.968

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.644
r_lrange_it	14.067
r_dihedral_angle_6_deg	13.451
r_scangle_it	8.473
r_dihedral_angle_2_deg	7.581
r_dihedral_angle_1_deg	7.376
r_mcangle_it	6.566
r_scbond_it	5.511
r_mcbond_it	4.11
r_angle_refined_deg	1.968
r_nbtor_refined	0.319
r_nbd_refined	0.257
r_symmetry_nbd_refined	0.255
r_symmetry_xyhbond_nbd_refined	0.245
r_xyhbond_nbd_refined	0.176
r_chiral_restr	0.138
r_bond_refined_d	0.007
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2502
Nucleic Acid Atoms
Solvent Atoms	15
Heterogen Atoms	71

Software

Software
Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
CrysalisPro	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 R01GM157729.