Experiment: 7CDK

X-RAY DIFFRACTION

Serial Crystallography (SX)

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

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		293	The lysozyme solution (40 mg/ml) in 10 mM Na-acetate, pH 4.6 was mixed with the same volume of 4 M Na-Malonate pH 3.1, 6% w/v PEG6000 and stirred for 20 minutes. The crystal growth was stopped by adding 2.4 M Na-Malonate pH 3.1, 3.6 % w/v PEG6000.

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.54

Symmetry
Space Group	P 43 21 2

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	PIXEL	DECTRIS EIGER X 16M		2019-11-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1	SPring-8	BL41XU

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

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	1.7	55.47	100	0.9808	5.87	181.9		13786			15.44

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	1.7	1.73			0.5264

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	FOURIER SYNTHESIS	FREE R-VALUE	4eta	1.7	55.47	1.34	13753	702	100	0.1947	0.1929	0.1944	0.2274	0.2289	16.35

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	13.2514
f_angle_d	0.7695
f_chiral_restr	0.0491
f_bond_d	0.0057
f_plane_restr	0.0036

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	49
Heterogen Atoms	8

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.

7CDK | pdb_00007cdk