7BHN | pdb_00007bhn

Crystal structure of hen egg white lysozyme using drop-on-drop SFX method - 2 s mixing with N-acetyl-D-glucosamine.

X-RAY DIFFRACTION

Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4ETA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		295	1 M citric acid, 20% (w/v) NaCl, 5% (w/v) PEG 6000, pH 3.0

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.804	α = 90
b = 78.804	β = 90
c = 38.002	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	308	CCD	RAYONIX MX300-HS		2019-07-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SACLA BEAMLINE BL2	1.24	SACLA	BL2

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1	acoustic droplet ejection	injection

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	1.45	55.72	100	0.98	0.136	68.773	125.38		21782			23.38

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	1.45	1.475			0.034	1.228	0.648

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4ETA	1.45	34.23	1.33	21738	1079	99.8	0.182	0.1811	0.18	0.1941	0.19	27.13

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	11.7716
f_angle_d	0.7651
f_chiral_restr	0.0786
f_bond_d	0.0051
f_plane_restr	0.0035

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	990
Nucleic Acid Atoms
Solvent Atoms	78
Heterogen Atoms	20

Software

Software
Software Name	Purpose
cctbx.xfel	data processing
PHASER	phasing
PHENIX	refinement

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.