8Z4R

The crystal structure of a Hydroquinone Dioxygenase PaD with substrate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		298	0.1 M HEPES 7.0; 24% PEG Smear Medium; 7% Tacsimate 7.0

Crystal Properties
Matthews coefficient	Solvent content
3.58	65.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.177	α = 90
b = 120.177	β = 90
c = 92.919	γ = 120

Symmetry
Space Group	P 62

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER2 X 9M		2023-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE TPS 05A	0.9998	NSRRC	TPS 05A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	1.81	25	99.6	0.999	29.4	5.8		69612

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.81	1.87			0.885

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.81	24.53	65962	3580	99.34	0.18833	0.18629	0.22491	RANDOM	35.014

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]
0.09	0.04		0.09		-0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.178
r_dihedral_angle_4_deg	21.134
r_dihedral_angle_3_deg	13.404
r_long_range_B_refined	6.696
r_long_range_B_other	6.668
r_dihedral_angle_1_deg	6.318
r_scangle_other	5.57
r_scbond_it	4.111
r_scbond_other	4.11
r_mcangle_it	3.787
r_mcangle_other	3.787
r_mcbond_it	3.223
r_mcbond_other	3.203
r_angle_refined_deg	1.734
r_angle_other_deg	1.477
r_chiral_restr	0.099
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001
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	3756
Nucleic Acid Atoms
Solvent Atoms	427
Heterogen Atoms	57

Software

Software
Software Name	Purpose
REFMAC	refinement
SAINT	data scaling
SAINT	data reduction
PHASER	phasing