9FTY | pdb_00009fty

Serial microseconds crystallography at ID29 using fixed-target (small foils): Proteinase K with 20 um spacing between X-ray pulses

X-RAY DIFFRACTION

Serial Crystallography (SX)

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	6.5	293	0.1 M MES pH 6.5, 0.5 M sodium nitrate, 0.1 M calcium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.72	α = 90
b = 68.72	β = 90
c = 108.97	γ = 90

Symmetry
Space Group	P 43 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	293	PIXEL	PSI JUNGFRAU 4M		2024-03-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.072	ESRF	ID29

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1	small foils	fixed target

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Split (All)	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	2	58.13	100	0.3207	3.94	133		18372			17.29

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.03			1.2812

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	2	58.13	1.34	18251	1823	99.65	0.2425	0.2403	0.2398	0.2622	0.2622	15.87

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	10.52
f_angle_d	0.4214
f_chiral_restr	0.0403
f_plane_restr	0.0031
f_bond_d	0.0015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1989
Nucleic Acid Atoms
Solvent Atoms	173
Heterogen Atoms	6

Software

Software
Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing

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.