6YRD | pdb_00006yrd

SFX structure of dye-type peroxidase DtpB in the ferryl state

X-RAY DIFFRACTION

Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		unpublished structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	7.5	293	6-10 mg/mL of protein in 50mM Sodium acetate, 150mM NaCl pH 5 was mixed with 150 mM MgCl2, 150 mM HEPES, 20% PEG 4000 pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.3	α = 90
b = 120	β = 90
c = 198.45	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	301	CCD	MPCCD		2019-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SACLA BEAMLINE BL2	1.13	SACLA	BL2

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1	silicon chip	fixed target

Fixed Target
Diffraction ID	Description	Sample Holding	Support Base	Motion control	Details	Sample Solvent
1	silicon chip				25600 apertures per chip

Measurement
Diffraction ID	Pulse Duration	Pulse Repetition Rate	Focal Spot Size	Pulse Energy	Photons Per Pulse
1	10 (fs)			11 (KeV)

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	1.75	102	100	0.984	0.109	6.1	1943		207440			28.4

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	1.75	1.8			0.423	0.887

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	unpublished structure	1.75	13	196370	10353	99.67	0.1682	0.1666	0.18	0.1988	0.21	RANDOM	33.628

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]
0.23			-0.36		0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.319
r_dihedral_angle_4_deg	17.361
r_dihedral_angle_3_deg	13.019
r_dihedral_angle_1_deg	6.771
r_angle_refined_deg	1.626
r_angle_other_deg	1.445
r_chiral_restr	0.073
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_gen_planes_other	0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.319
r_dihedral_angle_4_deg	17.361
r_dihedral_angle_3_deg	13.019
r_dihedral_angle_1_deg	6.771
r_angle_refined_deg	1.626
r_angle_other_deg	1.445
r_chiral_restr	0.073
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_gen_planes_other	0.006
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13904
Nucleic Acid Atoms
Solvent Atoms	880
Heterogen Atoms	279

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystFEL	data reduction
CrystFEL	data scaling
REFMAC	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.