9QQ4 | pdb_00009qq4

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293.15	The crystal was obtained from an initial screening using the sitting drop method performed on a 96-well MRC 2-well polystyrene crystallisation plate (SWISSCI, Switzerland) at 20 degree Celsius under a pure N2 atmosphere. The plate was filled with 90 uL crystallisation solution in the large reservoir and the purified protein solution concentrated to 4.4 mg/mL was spotted in the small reservoirs by mixing 0.5 uL purified protein with 0.5 uL crystallisation solution using an OryxNano robot (Douglas Instruments Ltd, UK). The crystallisation solution was composed of: 20 % v/v Jeffamine M-600 pH 7.0, and 100 mM HEPES pH 7.5. Once prepared, the plate was transferred to an anaerobic chamber containing an N2/H2 (97/3 percent) atmosphere for long-term storage. Prior liquid nitrogen freezing, the crystal was soaked in the crystallization solution supplemented with 25 % v/v glycerol for a few seconds.

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.83

Symmetry
Space Group	P 63

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 EIGER X 16M		2022-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.00000	SLS	X06SA

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	1.067	75.871	95.8	0.082	0.084	0.02	0.999	18.5	15.7		221484

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	1.067	1.129	58.4		1.052	1.154	0.466	0.654	1.7	5.9

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	1.07	75.87	1.35	221476	11147	87.86	0.1087	0.1078	0.1073	0.1254	0.1249	13.31

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	15.148
f_angle_d	1.267
f_chiral_restr	0.083
f_plane_restr	0.013
f_bond_d	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4423
Nucleic Acid Atoms
Solvent Atoms	924
Heterogen Atoms	250

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.

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 9QQ4 | pdb_00009qq4