Experiment: 9WS2

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3Q52

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	0.1 M MES, pH 6.3, 1.15 M ammonium tartrate, 0.2 M guanidine hydrochloride

Crystal Properties
Matthews coefficient	Solvent content
3.46	64.41

Symmetry
Space Group	P 63 2 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 PILATUS3 R 200K-A		2022-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54

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	1.9	50	99.8	0.147	0.152	0.037	0.999	20.4	15.8		39574

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.97	100		1.22	0.42	0.596	2	9.4

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.9	21.441	39515	1930	99.722	0.189	0.1881	0.1961	0.215	0.224	29.264

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]
0.022	0.011		0.022		-0.071

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.837
r_dihedral_angle_3_deg	12.751
r_lrange_it	8.894
r_lrange_other	8.795
r_dihedral_angle_1_deg	5.788
r_scangle_other	5.69
r_scangle_it	5.688
r_dihedral_angle_2_deg	5.519
r_scbond_it	3.524
r_scbond_other	3.522

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.837
r_dihedral_angle_3_deg	12.751
r_lrange_it	8.894
r_lrange_other	8.795
r_dihedral_angle_1_deg	5.788
r_scangle_other	5.69
r_scangle_it	5.688
r_dihedral_angle_2_deg	5.519
r_scbond_it	3.524
r_scbond_other	3.522
r_mcangle_it	3.469
r_mcangle_other	3.468
r_mcbond_it	2.292
r_mcbond_other	2.271
r_angle_refined_deg	1.38
r_angle_other_deg	0.492
r_symmetry_xyhbond_nbd_refined	0.219
r_nbd_refined	0.208
r_symmetry_nbd_other	0.186
r_xyhbond_nbd_refined	0.175
r_nbtor_refined	0.172
r_symmetry_nbd_refined	0.156
r_nbd_other	0.13
r_chiral_restr	0.075
r_symmetry_nbtor_other	0.075
r_chiral_restr_other	0.072
r_dihedral_angle_other_2_deg	0.01
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2352
Nucleic Acid Atoms
Solvent Atoms	281
Heterogen Atoms	38

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.

9WS2 | pdb_00009ws2