9I4Q | pdb_00009i4q

SSX structure of dye-type peroxidase DtpB from Streptomyces lividans

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	6YRJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		291	6-10 mg/ml of protein in 50 mm sodium acetate, 150 mm NaCl pH 5 mixed with 150 mM MgCl2, 150 mm HEPES, 20 % PEG 4000, pH 7.5, batch mode.

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.4	α = 90
b = 121.373	β = 90
c = 199.295	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	293	PIXEL	DECTRIS EIGER2 X CdTe 9M		2023-05-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.6200	Diamond	I24

Serial Crystallography

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

Fixed Target
Diffraction ID	Description	Sample Holding	Support Base	Motion control	Details	Sample Solvent
1	Oxford silicon chip			Geobrick and Smaract

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

Data Reduction
Diffraction ID	Frames Indexed	Crystal Hits	Frames Indexed	Latices Merged
1

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	2.75	103.66	100	0.916	0.303	5.1	22.2		55276

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	2.75	2.8			0.297	1.018

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	2.75	79.397	55273	2784	99.989	0.193	0.1905	0.1904	0.2439	0.244	38.853

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]
0.159			0.069		-0.228

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.136
r_dihedral_angle_6_deg	11.626
r_dihedral_angle_1_deg	6.622
r_lrange_it	6.139
r_dihedral_angle_2_deg	4.316
r_scangle_it	3.59
r_mcangle_it	2.899
r_scbond_it	2.077
r_mcbond_it	1.632
r_angle_refined_deg	1.119
r_nbtor_refined	0.297
r_symmetry_nbd_refined	0.224
r_nbd_refined	0.192
r_xyhbond_nbd_refined	0.133
r_symmetry_xyhbond_nbd_refined	0.122
r_chiral_restr	0.083
r_bond_refined_d	0.003
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13935
Nucleic Acid Atoms
Solvent Atoms	247
Heterogen Atoms	260

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
xia2	data reduction
xia2	data scaling
MOLREP	phasing
Coot	model building