6JXP

Room temperature structure of lysozyme delivered in LCP by serial millisecond crystallography

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6IRJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	SMALL TUBES		293.5	sodium acetate, PEG 8000, NaCl

Crystal Properties
Matthews coefficient	Solvent content
1.79	31.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.41	α = 90
b = 78.41	β = 90
c = 37.93	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	298.15	PIXEL	DECTRIS PILATUS3 S 6M		2019-02-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 11C	0.97942	PAL/PLS	11C

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1		injection

Data Reduction
Diffraction ID	Frames Indexed	Crystal Hits	Total Frames
1	19411	24258	40000

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	1.56	78.7	99.93	0.991	0.0987	6	318.4		17418			22.87

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.56	1.61	99.23		0.436	0.8866	1.26

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6IRJ	1.56	55.44	1.34	17361	1738	99.84	0.1708	0.1675	0.2003	31.94

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	12.1477
f_angle_d	1.0222
f_chiral_restr	0.0609
f_bond_d	0.0102
f_plane_restr	0.0055

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	88
Heterogen Atoms	2

Software

Software
Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystFEL	data reduction
CrystFEL	data scaling
PHENIX	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 R01GM133198.