9TVN | pdb_00009tvn

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	6.5	293.15	10 mg/ml protein and 0.12 M monosaccharides mix (0.2 M D-glucose, 0.2 M D-mannose, 0.2 M D-galactose, 0.2 M L-fucose, 0.2 M D-xylose, 0.2 M N-acetyl-D-glucosamine), 0.1 M buffer system 1 pH 6.5 (0.5 M imidazole, 0.5 M MES monohydrate acid), 50% (v/v) precipitant mix 2 (40% (v/v) ethylene glycol, 20% (w/v) PEG 8000)

Symmetry
Space Group	P 21 21 21

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 PILATUS4 XE 4M		2025-03-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.96546	ESRF	MASSIF-1

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	2.1	46.22	100	0.152	0.166	0.065	0.996	10.6	6.5		154277

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	2.1	2.16		100	1.166	1.271	0.501	0.541		6.4

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.1	46.219	23900	1121	99.958	0.189	0.1858	0.2552	RANDOM	29.387

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]
-0.643			0.787		-0.143

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.991
r_dihedral_angle_6_deg	14.413
r_dihedral_angle_2_deg	11.507
r_lrange_it	7.036
r_lrange_other	7.022
r_dihedral_angle_1_deg	6.233
r_scangle_it	5.833
r_scangle_other	5.832
r_scbond_it	3.799
r_scbond_other	3.799

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.991
r_dihedral_angle_6_deg	14.413
r_dihedral_angle_2_deg	11.507
r_lrange_it	7.036
r_lrange_other	7.022
r_dihedral_angle_1_deg	6.233
r_scangle_it	5.833
r_scangle_other	5.832
r_scbond_it	3.799
r_scbond_other	3.799
r_mcangle_it	3.368
r_mcangle_other	3.367
r_mcbond_it	2.384
r_mcbond_other	2.379
r_angle_refined_deg	1.812
r_angle_other_deg	0.579
r_chiral_restr_other	0.271
r_nbd_refined	0.233
r_nbd_other	0.225
r_symmetry_nbd_other	0.198
r_symmetry_nbd_refined	0.195
r_nbtor_refined	0.186
r_symmetry_xyhbond_nbd_refined	0.184
r_xyhbond_nbd_refined	0.183
r_chiral_restr	0.082
r_symmetry_nbtor_other	0.081
r_symmetry_xyhbond_nbd_other	0.041
r_dihedral_angle_other_2_deg	0.019
r_bond_refined_d	0.008
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	3151
Nucleic Acid Atoms
Solvent Atoms	198
Heterogen Atoms	41

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.