9FB7 | pdb_00009fb7

Dye-decolourising peroxidase DtpB (280 kGy)

X-RAY DIFFRACTION

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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	7.5	293	6.2 mg/mL of protein in 20 mM NaPi, 150 mM NaCl pH 7 was mixed with 125 mM MgCl2, 125 mM HEPES, 18% PEG 4000 pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.891	α = 90
b = 121.924	β = 90
c = 199.572	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 PILATUS 6M		2019-09-19	M	SINGLE WAVELENGTH

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

Serial Crystallography

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

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		21216

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	2.02	40.12	100	0.9876	0.126	1.6	85.2		139296

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	2.02	2.07			0.57	0.567	0.5

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	2.02	40.12	132270	6929	99.95	0.23019	0.22874	0.2318	0.25782	0.2571	RANDOM	35.109

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]
-0.01			0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.527
r_dihedral_angle_2_deg	12.958
r_long_range_B_other	8.874
r_long_range_B_refined	8.873
r_dihedral_angle_1_deg	7.616
r_scangle_other	7.401
r_mcangle_it	5.77
r_mcangle_other	5.769
r_scbond_it	4.908
r_scbond_other	4.908
r_mcbond_it	3.814
r_mcbond_other	3.812
r_angle_refined_deg	2.16
r_angle_other_deg	0.727
r_chiral_restr	0.091
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_gen_planes_other	0.005
r_bond_other_d	0.001
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	13801
Nucleic Acid Atoms
Solvent Atoms	73
Heterogen Atoms	272

Software

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