9SQ3 | pdb_00009sq3

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9SPZ

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293.15	Samples were centrifuged at 13,000 x g for 3 min to remove macro-aggregates and dust, and crystallised inside an anaerobic chamber (N2/H2 (97:3%) atmosphere, 20 degree Celsius). Crystallisation was done by the sitting drop method in 96-Well MRC 2-Drop polystyrene Crystallisation Plates (SWISSCI) containing 90 uL of crystallisation solution in the reservoir. Crystals were obtained by mixing 0.7 uL of crystallisation solution with 0.7 uL of protein sample at 22.4 mg.ml-1. The crystallisation solution contained the following: 30 % v/v 2-methyl-2,4-pentanediol, 100 mM Tris pH 8.5, 500 mM Sodium chloride and 8 % w/v Polyethylene glycol 8,000 (Crystallisation solution of the JBScreen Wizard form Jena Bioscience, Germany).

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.76

Symmetry
Space Group	P 1

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 PILATUS 6M		2023-05-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM07	0.97951	ESRF	BM07

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	1.21	101.86	92	0.074	0.079	0.03	0.999	12.9	7.1		371908

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	1.21	1.35	74.5		1.071	1.154	0.425	0.669	1.7	7.3

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.21	33.62	1.96	371077	18775	61.95	0.1221	0.1208	0.1288	0.146	0.1497	17.71

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.877
f_angle_d	1.472
f_chiral_restr	0.111
f_plane_restr	0.021
f_bond_d	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14906
Nucleic Acid Atoms
Solvent Atoms	2023
Heterogen Atoms	291

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.