8RGY | pdb_00008rgy

Serial synchrotron in plate room temperature structure of Dye Type Peroxidase Aa, 8 drops merged

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	7	291	1:3 v/v ratio of 10 mg/ml protein in 20 mM sodium phosphate, 150 mM NaCl, pH 7.0 and a mother liquor solution (12% v/v PEG 3350, 100 mM HEPES, pH 7.0)

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.456	α = 90
b = 67.759	β = 105.69
c = 74.707	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	298	PIXEL	DECTRIS EIGER2 X 4M		2023-10-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE VMXi	0.775	Diamond	VMXi

Serial Crystallography

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

Fixed Target
Diffraction ID	Description	Sample Holding	Support Base	Motion control	Details	Sample Solvent
1	Mitegen in situ-1 plate

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	2.07	69.76	97.74	0.927	0.285	12.6	28.7		42538			25.18

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	2.07	2.144			0.329	1.759

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	FREE R-VALUE	2.07	69.76	1.33	41631	2104	97.75	0.2259	0.2233	0.22	0.2748	0.27	27.62

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	15.5665
f_angle_d	0.6177
f_chiral_restr	0.04
f_plane_restr	0.0044
f_bond_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5476
Nucleic Acid Atoms
Solvent Atoms	411
Heterogen Atoms	86

Software

Software
Software Name	Purpose
Coot	model building
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHENIX	phasing

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.