Experiment: 9VVB

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, methylcellulose 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 pH5.4, 5 mM MTA

Crystal Properties
Matthews coefficient	Solvent content
2.28788519	46.2719612

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	353	PIXEL	DECTRIS EIGER X 16M		2025-06-26	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	1.83	44.45	100	0.145	0.161	0.069	0.997	10.7	10.1		25314

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)
	1.83	1.87	100		1.066	1.19	0.525	0.705	2.9	9.8

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	1.83	44.45	25313	1262	99.968	0.142	0.1402	0.1522	0.1678	0.1747	28.902

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]
0.155	0.077		0.155		-0.503

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.985
r_dihedral_angle_3_deg	14.078
r_lrange_other	9.967
r_lrange_it	9.964
r_dihedral_angle_2_deg	8.093
r_scangle_other	8.081
r_scangle_it	8.075
r_dihedral_angle_1_deg	7.274
r_scbond_other	5.052
r_scbond_it	5.049

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.985
r_dihedral_angle_3_deg	14.078
r_lrange_other	9.967
r_lrange_it	9.964
r_dihedral_angle_2_deg	8.093
r_scangle_other	8.081
r_scangle_it	8.075
r_dihedral_angle_1_deg	7.274
r_scbond_other	5.052
r_scbond_it	5.049
r_mcangle_it	3.981
r_mcangle_other	3.979
r_mcbond_it	2.764
r_mcbond_other	2.764
r_angle_refined_deg	1.805
r_angle_other_deg	0.606
r_nbd_refined	0.215
r_symmetry_nbd_other	0.196
r_nbd_other	0.185
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.141
r_symmetry_xyhbond_nbd_refined	0.137
r_symmetry_nbd_refined	0.117
r_chiral_restr	0.089
r_symmetry_nbtor_other	0.085
r_dihedral_angle_other_2_deg	0.022
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2142
Nucleic Acid Atoms
Solvent Atoms	38
Heterogen Atoms	25

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.

9VVB | pdb_00009vvb