9TVK | pdb_00009tvk

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	7.5	293.15	15 mg/ml protein and 0.09 M halogens mix (0.3 M sodium fluoride, 0.3 M sodium bromide, 0.3 M sodium iodide), 0.1 M buffer system 2 pH 7.5 (0.5 M sodium Hepes, 0.5 M bicine), 50% (v/v) precipitant mix 4 (25% (v/v) MPD, 25% (w/v) PEG 1000, 25% (w/v) PEG 3350)

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.17

Symmetry
Space Group	P 41 3 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 EIGER X 9M		2025-09-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.8731281579802835	ESRF	ID23-2

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (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	2.398	106.411	100	0.144	0.996	8.3	6.6		23456

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.49			1.153	0.615

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-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.398	106.411	23397	1180	99.898	0.187	0.1844	0.2374	51.862

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.53
r_dihedral_angle_6_deg	15.128
r_lrange_it	12.736
r_lrange_other	12.691
r_scangle_it	10.081
r_scangle_other	10.079
r_mcangle_it	7.958
r_mcangle_other	7.955
r_dihedral_angle_2_deg	7.669
r_dihedral_angle_1_deg	7.318

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.53
r_dihedral_angle_6_deg	15.128
r_lrange_it	12.736
r_lrange_other	12.691
r_scangle_it	10.081
r_scangle_other	10.079
r_mcangle_it	7.958
r_mcangle_other	7.955
r_dihedral_angle_2_deg	7.669
r_dihedral_angle_1_deg	7.318
r_scbond_it	6.65
r_scbond_other	6.649
r_mcbond_it	5.535
r_mcbond_other	5.459
r_angle_refined_deg	1.918
r_angle_other_deg	0.656
r_symmetry_xyhbond_nbd_other	0.458
r_symmetry_nbd_refined	0.265
r_nbd_refined	0.23
r_symmetry_nbd_other	0.196
r_symmetry_xyhbond_nbd_refined	0.187
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.185
r_nbd_other	0.172
r_metal_ion_refined	0.119
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.08
r_bond_refined_d	0.008
r_dihedral_angle_other_2_deg	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2968
Nucleic Acid Atoms
Solvent Atoms	173
Heterogen Atoms	40

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.