8S2V | pdb_00008s2v

SSX structure of Lysozyme grown in microfluidic droplets

X-RAY DIFFRACTION

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Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6H79

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROFLUIDIC	3	294	20 mg/mL Lysozyme dissolved in 20 mM sodium acetate pH 4.6 Precipitant: 6% PEG 6000 (W/V), 3.4M NaCl and 1M sodium acetate pH 3.0

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.9	α = 90
b = 78.9	β = 90
c = 37.9	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		2023-01-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.07	ESRF	ID29

Serial Crystallography

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

Data Reduction
Diffraction ID	Frames Indexed	Crystal Hits	Frames Indexed	Latices Merged
1	22304	22815	22304

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	1.8	78.9	100	0.99	17.2	464		11607			24.06

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	1.8	1.83	100		0.44	0.9	51.94

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.8	55.853	11567	581	99.991	0.148	0.1456	0.16	0.1897	0.2	32.594

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]
0.001			0.001		-0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.028
r_dihedral_angle_6_deg	13.988
r_lrange_it	7.614
r_lrange_other	7.613
r_scangle_it	6.812
r_scangle_other	6.807
r_dihedral_angle_1_deg	6.733
r_dihedral_angle_2_deg	5.959
r_scbond_it	4.351
r_scbond_other	4.348
r_mcangle_other	3.185
r_mcangle_it	3.149
r_mcbond_it	2.497
r_mcbond_other	2.427
r_angle_refined_deg	1.767
r_angle_other_deg	0.601
r_nbd_refined	0.239
r_symmetry_nbd_other	0.212
r_nbtor_refined	0.205
r_xyhbond_nbd_refined	0.181
r_nbd_other	0.153
r_symmetry_xyhbond_nbd_refined	0.138
r_chiral_restr	0.083
r_symmetry_nbtor_other	0.083
r_symmetry_nbd_refined	0.043
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	66
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystFEL	data reduction
CrystFEL	data scaling
MOLREP	phasing