9S5B | pdb_00009s5b

Fragment screening of FosAKP, room-temperature structure, ground state, small unit cell

X-RAY DIFFRACTION

Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5V91

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	291	25 mg/mL FosAKP in 10 mM Hepes, pH 7.5, 75 mM NaCl was supplemented with 6 mM MnCl2 and mixed with an equal volume of 16% (w/v) PEG3350, 0.25 M MgCl2, 0.2 M KBr, 0.1 M BisTris, pH 5.5 and 1/10 volume of seed stock in 26% (w/v) PEG3350, 0.25 M MgCl2, 0.2 M KBr, 0.1 M BisTris, pH 5.5. From this, approximately 14 uL were added per window of the fixed-target chip. The sample holder was then inserted for into a 3D-printed crystal growth chamber with 3 mL of precipitant solution in the bottom for vapor-diffusion crystallization and incubated at 20C. Before data collection sample holder was removed from the crystal growth chamber and excess precipitant was removed by blotting through the micropores of the membranes, before 10 uL of crystallization solution with 5 % DMSO were pipetted to the crystals in the individual compartments. Sample holders were then placed back into the growths vessel and incubated for 24h. Before data collection blotting was repeated for removal of excess liquid in order to minimize background scattering. Sample holders were then equipped with a protective cover to prevent them from drying-out and stored in a humid atmosphere. Compound addition and liquid removal were conducted in a glove box with >95% rel. humidity.

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.28	α = 90
b = 90.83	β = 90
c = 45.26	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	296	PIXEL	DECTRIS PILATUS 6M-F	CRL	2023-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P09 HiPhaX	0.7749	PETRA III, DESY	P09 HiPhaX

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1	fixed target using micro-patterned chip	fixed target

Fixed Target
Diffraction ID	Description	Sample Holding	Support Base	Motion control	Details	Sample Solvent
1	Crystals were directly grown on the chip surface. Excess liquid was removed by blotting in an glove box to maintain rel. humidity levels >95%.	micro-patterned chip	kinematic mount	Roadrunner Goniometer

Data Reduction
Diffraction ID	Frames Indexed	Crystal Hits	Frames Indexed	Latices Merged
1	42361	51602	42361

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.5	90.84	100	0.99	8.1	219		46568			14.14

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.55	100		0.519	1.33	38.1

Refinement

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	1.5	55.09	1.34	46463	2227	99.88	0.138	0.1363	0.1375	0.1718	0.1728	19.9

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	14.9423
f_angle_d	0.8725
f_chiral_restr	0.053
f_plane_restr	0.0081
f_bond_d	0.0059

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2162
Nucleic Acid Atoms
Solvent Atoms	235
Heterogen Atoms	2

Software

Software
Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHENIX	phasing
Coot	model building

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.