8ZI8

Terephthalate 1,2-cis-dihydrodioldehydrogenase/Decarboxylase in complex with 2,5-Dihydroxybenzoate.

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	8	295	4% v/v Tacsimate pH 6.0 12% w/v Polyethylene glycol 3,350

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.549	α = 90
b = 94.717	β = 90
c = 166.714	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	RIGAKU HyPix-6000HE		2023-01-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54

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	2.65	27.23	99.8	0.993	6.9	7.1		40549

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	2.65	2.76	100		0.788	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	40475	2000	99.663	0.262	0.2604	0.2949	3.479

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]
-2.439			3.645		-1.206

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	19.009
r_dihedral_angle_3_deg	14.377
r_dihedral_angle_6_deg	13.806
r_dihedral_angle_1_deg	6.183
r_lrange_it	4.122
r_lrange_other	4.01
r_rigid_bond_restr	3.649
r_angle_refined_deg	1.343
r_mcangle_it	1.128
r_mcangle_other	1.128
r_scangle_it	1.115
r_scangle_other	1.115
r_mcbond_it	0.682
r_mcbond_other	0.681
r_scbond_it	0.677
r_scbond_other	0.677
r_angle_other_deg	0.471
r_nbd_refined	0.232
r_symmetry_xyhbond_nbd_refined	0.214
r_symmetry_nbd_other	0.201
r_xyhbond_nbd_refined	0.197
r_nbtor_refined	0.165
r_nbd_other	0.165
r_symmetry_nbd_refined	0.158
r_metal_ion_refined	0.132
r_ncsr_local_group_4	0.125
r_ncsr_local_group_5	0.114
r_ncsr_local_group_1	0.105
r_ncsr_local_group_2	0.104
r_ncsr_local_group_6	0.101
r_ncsr_local_group_3	0.079
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.067
r_bond_refined_d	0.006
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	9184
Nucleic Acid Atoms
Solvent Atoms	121
Heterogen Atoms	40

Software

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