8S2U | pdb_00008s2u

SSX structure of Lysozyme grown in batch conditions

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	BATCH MODE	3	294	Protein dissolved in 20 mM sodium acetate pH 4.6 Protein and precipitant mixed in a 1:4 ratio Precipitant solution: 6% PEG 6000 (w/v), 3.4M NaCl and 1M sodium acetate pH 3.0

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79	α = 90
b = 79	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	29954	34032	29954

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	79	100	0.99	13.5	438		11636			30.46

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		0.49	0.2	47.67

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	55.924	11597	581	99.991	0.173	0.1706	0.1787	0.2307	0.2424	38.199

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]
-0.004			-0.004		0.008

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.297
r_dihedral_angle_3_deg	12.871
r_dihedral_angle_2_deg	8.961
r_lrange_it	8.004
r_lrange_other	7.97
r_dihedral_angle_1_deg	6.997
r_scangle_it	6.642
r_scangle_other	6.638
r_scbond_it	4.325
r_scbond_other	4.321
r_mcangle_other	3.453
r_mcangle_it	3.43
r_mcbond_other	2.721
r_mcbond_it	2.719
r_angle_refined_deg	1.551
r_angle_other_deg	0.562
r_nbd_refined	0.222
r_symmetry_nbd_other	0.202
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.175
r_nbd_other	0.118
r_symmetry_xyhbond_nbd_refined	0.105
r_symmetry_nbd_refined	0.091
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.076
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
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	59
Heterogen Atoms	2

Software

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