Experiment: 6Q3E

Dye type peroxidase Aa from Streptomyces lividans: 274.4 kGy structure

X-RAY DIFFRACTION

Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6I43

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	8	293	7 mg/ml protein mixed with 17% PEG 1500 and 67 mM MIB buffer (comprising imidazole, malonate and boric acid)

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.068	α = 90
b = 68.384	β = 105.85
c = 75.097	γ = 90

Symmetry
Space Group	P 1 21 1

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	DECTRIS PILATUS3 6M		2018-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9686	Diamond	I24

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1	Silicon nitride chips	fixed target

Measurement
Diffraction ID	Pulse Duration	Pulse Repetition Rate	Focal Spot Size	Pulse Energy	Photons Per Pulse
1	undefined (fs)			undefined (KeV)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.03	44.7	100	0.765	0.969	0.179	2.02	44.5		46140

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.03	2.07	99.6		0.859	0.506	0.783	0.5	11.4

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	THROUGHOUT	6I43	2.03	37.386	1.35	46139	1990	99.97	0.1846	0.1816	0.1821	0.2491	0.2498	32.5936

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5542
Nucleic Acid Atoms
Solvent Atoms	211
Heterogen Atoms	146

Software

Software
Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
cctbx.prime	data scaling
MOLREP	phasing