Experiment: 9XUI

X-RAY DIFFRACTION

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

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	0.2M Magnesium chloride hexahydrate; 0.1M Sodium HEPES pH 7.5; 30% PEG 400

Crystal Properties
Matthews coefficient	Solvent content
3.39	63.76

Symmetry
Space Group	P 61

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		2024-07-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE TPS 07A	0.9762	NSRRC	TPS 07A

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	1.38	25	98.3	0.058	0.063	0.025	0.996	11	5.9		79329

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	1.38	1.43	95.4		0.626	0.682	0.267	0.873		6.1

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 (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	1.38	24.74	75309	3970	98.29	0.13241	0.13145	0.1316	0.15102	0.1513	RANDOM	19.271

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]
0.33	0.17		0.33		-1.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.576
r_dihedral_angle_4_deg	23.081
r_dihedral_angle_3_deg	10.498
r_dihedral_angle_1_deg	6.449
r_long_range_B_refined	5.527
r_long_range_B_other	5.178
r_scangle_other	4.335
r_scbond_other	2.936
r_scbond_it	2.935
r_mcangle_other	2.214

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.576
r_dihedral_angle_4_deg	23.081
r_dihedral_angle_3_deg	10.498
r_dihedral_angle_1_deg	6.449
r_long_range_B_refined	5.527
r_long_range_B_other	5.178
r_scangle_other	4.335
r_scbond_other	2.936
r_scbond_it	2.935
r_mcangle_other	2.214
r_mcangle_it	2.206
r_angle_refined_deg	2.08
r_angle_other_deg	1.657
r_mcbond_it	1.422
r_mcbond_other	1.396
r_chiral_restr	0.126
r_bond_refined_d	0.017
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1995
Nucleic Acid Atoms
Solvent Atoms	393
Heterogen Atoms	10

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

9XUI | pdb_00009xui