8PXQ | pdb_00008pxq

SFX Ferric structure of Y389F variant of A type dye-decolourising peroxidase DtpAa

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	6I43

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	7	293	1:1 v/v ratio of a solution containing 6.2 mg/ml Y389F DtpAa in 20 mM sodium phosphate, 150 mM NaCl pH 7 with a precipitant solution consisting of 100 mM HEPES pH 7 and 15% PEG 6000 to give a final volume of 400 ul.

Crystal Properties
Matthews coefficient	Solvent content
2	38.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.567	α = 90
b = 68.14	β = 105.5
c = 74.8	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	CCD	RAYONIX MX225-HS		2022-05-11	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		fixed target

Fixed Target
Diffraction ID	Description	Sample Holding	Support Base	Motion control	Details	Sample Solvent
1		Silicon chip

Measurement
Diffraction ID	Pulse Duration	Pulse Repetition Rate	Focal Spot Size	Pulse Energy	Photons Per Pulse
1	10 (fs)	30		11 (KeV)

Data Reduction
Diffraction ID	Frames Indexed	Crystal Hits	Frames Indexed	Latices Merged
1		11101

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	1.7	48.85	100	0.879	0.279	3.13	70.4		73582

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	1.7	1.73			0.514	0.753

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.7	48.85	73582	3803	99.99	0.1688	0.16695	0.1775	0.20502	0.2117	RANDOM	18.05

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]
0.28		-0.06	-0.37		0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	17.383
r_dihedral_angle_3_deg	13.69
r_dihedral_angle_1_deg	6.74
r_long_range_B_refined	5.225
r_long_range_B_other	5.217
r_scangle_other	4.779
r_scbond_other	3.34
r_scbond_it	3.339
r_mcangle_other	2.929
r_mcangle_it	2.927
r_mcbond_it	2.24
r_mcbond_other	2.219
r_angle_refined_deg	1.924
r_angle_other_deg	0.649
r_chiral_restr	0.097
r_bond_refined_d	0.014
r_gen_planes_refined	0.013
r_gen_planes_other	0.005
r_bond_other_d	0.002
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5510
Nucleic Acid Atoms
Solvent Atoms	361
Heterogen Atoms	43

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystFEL	data reduction
CrystFEL	data scaling
REFMAC	phasing