Experiment: 9VSS

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1WTA

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	COUNTER-DIFFUSION	5.4	293.2	The mixture of protein solution and agarose, methylcellurose was filled into a glass capillary, and the capillary was immersed in the reservoir solution for crystallization. The composition of the reservoir solution was as follows. 15%(v/v)PEG#200, 0.1M phosphate citrate pH 5.4, 5mM MTA

Crystal Properties
Matthews coefficient	Solvent content
2.27571559	45.9846382

Symmetry
Space Group	H 3 2

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	363	PIXEL	DECTRIS EIGER X 16M		2025-07-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	0.98	Photon Factory	BL-17A

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	1.79	44.35	99.9	0.224	0.252	0.112	0.985	12.4	9.6		26844

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)
	1.79	1.83	100		1.22	1.368	0.614	0.704	3.2	9.5

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	1WTA	1.79	44.35	26842	1391	99.903	0.151	0.1494	0.1593	0.1759	0.1864	28.444

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]
0.021	0.01		0.021		-0.068

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.826
r_dihedral_angle_3_deg	14.104
r_lrange_it	10.159
r_lrange_other	10.159
r_dihedral_angle_2_deg	8.531
r_scangle_it	7.712
r_scangle_other	7.71
r_dihedral_angle_1_deg	6.939
r_scbond_it	4.885
r_scbond_other	4.884

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.826
r_dihedral_angle_3_deg	14.104
r_lrange_it	10.159
r_lrange_other	10.159
r_dihedral_angle_2_deg	8.531
r_scangle_it	7.712
r_scangle_other	7.71
r_dihedral_angle_1_deg	6.939
r_scbond_it	4.885
r_scbond_other	4.884
r_mcangle_it	4.184
r_mcangle_other	4.183
r_mcbond_it	2.789
r_mcbond_other	2.788
r_angle_refined_deg	1.852
r_angle_other_deg	0.62
r_nbd_refined	0.21
r_symmetry_nbd_refined	0.208
r_nbd_other	0.204
r_symmetry_nbd_other	0.199
r_nbtor_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.14
r_xyhbond_nbd_refined	0.134
r_chiral_restr	0.089
r_symmetry_nbtor_other	0.086
r_dihedral_angle_other_2_deg	0.054
r_symmetry_xyhbond_nbd_other	0.051
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2140
Nucleic Acid Atoms
Solvent Atoms	41
Heterogen Atoms	32

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.

9VSS | pdb_00009vss