8RPM

Lysozyme structure based on automated real-time serial crystallography data processing using CrystFEL

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROFLUIDIC	3.5	295	Just in-time crystallization (JINXED): a lysozyme solution in acetate buffer (pH 3.5) was mixed with crystallization solution on a running conveyor belt using 3D printed micro nozzles. Crystallization solution: N,N',N'',N''',N'''',N'''''-Hexaacetyl chitohexaose in 33 mM acetate buffer, pH3.5, 6.67% (w/v) PEG4000, 2.07 M NaCl, 6.67% DMSO

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.2	α = 90
b = 79.2	β = 90
c = 38	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	295	PIXEL	DECTRIS EIGER X 16M		2023-06-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.033	PETRA III, DESY	P11

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1	JINXED on TapeDrive	injection

Data Reduction
Diffraction ID	Frames Indexed	Crystal Hits	Total Frames
1			200000

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	1.8	79.365	100	0.98	0.117	5.292	373.9		11716

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	1.8	1.864	100		0.446	1.115	0.94	248.5

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.8	56	10264	637	93.31	0.18695	0.18466	0.22215	RANDOM	34.619

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]
-0.26			-0.26		0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	11.44
r_long_range_B_other	9.602
r_long_range_B_refined	9.599
r_scangle_other	8.456
r_dihedral_angle_1_deg	7.007
r_scbond_it	5.882
r_scbond_other	5.874
r_dihedral_angle_2_deg	4.72
r_mcangle_other	4.64
r_mcangle_it	4.594
r_mcbond_it	3.779
r_mcbond_other	3.756
r_angle_refined_deg	1.433
r_angle_other_deg	0.491
r_chiral_restr	0.072
r_gen_planes_refined	0.006
r_bond_refined_d	0.005
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	71
Heterogen Atoms	3

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
PDB-REDO	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHENIX	phasing