Experiment: 9W5Y

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	8.5	293.15	200 mM Lithium sulfate 100 mM TRIS-HCl 30% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.52

Symmetry
Space Group	I 2 2 2

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 PILATUS3 S 6M		2023-05-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0000	Photon Factory	BL-5A

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.66	41.47	100	0.063	0.019	1	23.3	12.6		12321

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.66	2.79	100		1.01	0.279	0.898	2.6	13.6

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	2.66	41.47	11646	636	99.65	0.21711	0.21466	0.2177	0.26165	0.267	RANDOM	87.122

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]
-2.5			-4.51		7.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.302
r_long_range_B_refined	7.522
r_long_range_B_other	7.521
r_dihedral_angle_1_deg	6.938
r_dihedral_angle_2_deg	5.853
r_scangle_other	5.129
r_mcangle_it	4.096
r_mcangle_other	4.095
r_scbond_it	3.673
r_scbond_other	3.331

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.302
r_long_range_B_refined	7.522
r_long_range_B_other	7.521
r_dihedral_angle_1_deg	6.938
r_dihedral_angle_2_deg	5.853
r_scangle_other	5.129
r_mcangle_it	4.096
r_mcangle_other	4.095
r_scbond_it	3.673
r_scbond_other	3.331
r_mcbond_it	2.741
r_mcbond_other	2.738
r_angle_refined_deg	1.216
r_angle_other_deg	0.424
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
r_dihedral_angle_4_deg
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	2438
Nucleic Acid Atoms
Solvent Atoms	9
Heterogen Atoms	121

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.

9W5Y | pdb_00009w5y