8ZJ7

Terephthalate 1,2-cis-dihydrodioldehydrogenase/Decarboxylase in complex with 3,4-Dihydroxybenzoate and NAD.

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, SITTING DROP	7.4	295	0.2 M Potassium sodium tartrate tetrahydrate 20% w/v Polyethylene glycol 3,350 pH 7.4

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.303	α = 90
b = 98.148	β = 90
c = 168.036	γ = 90

Symmetry
Space Group	P 2 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	100	PIXEL	DECTRIS EIGER2 X 16M		2022-09-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.885	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.26	168	99.8	0.116	0.127	0.052	0.998	10.5	5.8		42519

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.26	2.3	100		1.257	1.372	0.543	0.624	2.1

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.65	24.001	42519	2135	99.548	0.185	0.1813	0.2517	49.71

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]
-6.9			11.944		-5.044

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	49.141
r_lrange_other	48.092
r_scangle_it	19.689
r_scangle_other	19.683
r_mcangle_it	16.897
r_mcangle_other	16.896
r_dihedral_angle_3_deg	15.016
r_dihedral_angle_6_deg	13.626
r_scbond_it	13.065
r_scbond_other	13.057
r_mcbond_it	11.088
r_mcbond_other	11.086
r_dihedral_angle_2_deg	8.795
r_dihedral_angle_1_deg	5.997
r_rigid_bond_restr	5.594
r_dihedral_angle_other_2_deg	1.763
r_angle_refined_deg	1.502
r_angle_other_deg	0.49
r_symmetry_xyhbond_nbd_refined	0.4
r_symmetry_xyhbond_nbd_other	0.266
r_symmetry_nbd_refined	0.239
r_nbd_refined	0.225
r_symmetry_nbd_other	0.201
r_xyhbond_nbd_refined	0.186
r_nbtor_refined	0.168
r_nbd_other	0.16
r_ncsr_local_group_5	0.099
r_ncsr_local_group_3	0.097
r_ncsr_local_group_1	0.096
r_ncsr_local_group_6	0.094
r_ncsr_local_group_2	0.093
r_ncsr_local_group_4	0.089
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.068
r_metal_ion_refined	0.035
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9182
Nucleic Acid Atoms
Solvent Atoms	122
Heterogen Atoms	128

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
Aimless	data scaling
MOLREP	phasing