9WON | pdb_00009won

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6WRH

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	291	0.2 M Ammonium sulfate, 0.1 M tri-Sodium citrate (pH 5.6) and 15% w/v PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
3.02	59.39

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 EIGER2 X 9M		2023-09-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE TPS 05A	1.00003	NSRRC	TPS 05A

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	1.89	48.83	99.7	0.123	0.136	0.058	0.999	11.5	9.9		70080

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	1.89	1.93	99.5		1.229	1.372	0.6	0.88	2.2	9.5

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-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	1.89	48.742	69994	3465	99.667	0.222	0.22172	0.2213	0.2356	0.2305	0.2434	RANDOM	30.251

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]
-3.059			4.966		-1.907

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	18.002
r_dihedral_angle_3_deg	13.718
r_dihedral_angle_1_deg	5.997
r_lrange_it	4.954
r_lrange_other	4.654
r_scangle_it	2.664
r_scangle_other	2.663
r_mcangle_other	2.223
r_mcangle_it	2.222
r_scbond_it	1.577

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	18.002
r_dihedral_angle_3_deg	13.718
r_dihedral_angle_1_deg	5.997
r_lrange_it	4.954
r_lrange_other	4.654
r_scangle_it	2.664
r_scangle_other	2.663
r_mcangle_other	2.223
r_mcangle_it	2.222
r_scbond_it	1.577
r_scbond_other	1.577
r_mcbond_it	1.372
r_mcbond_other	1.371
r_angle_refined_deg	1.358
r_angle_other_deg	0.893
r_dihedral_angle_2_deg	0.55
r_nbd_other	0.237
r_nbd_refined	0.194
r_symmetry_nbd_other	0.194
r_symmetry_xyhbond_nbd_refined	0.189
r_xyhbond_nbd_refined	0.174
r_nbtor_refined	0.159
r_symmetry_nbd_refined	0.127
r_metal_ion_refined	0.103
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.058
r_bond_refined_d	0.014
r_gen_planes_other	0.006
r_gen_planes_refined	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5016
Nucleic Acid Atoms
Solvent Atoms	703
Heterogen Atoms	186

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.