8ZJ3 | pdb_00008zj3

Terephthalate 1,2-cis-dihydrodioldehydrogenase/Decarboxylase in complex with 4-Hydroxybenzoate.

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
2.61	53.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.831	α = 90
b = 94.332	β = 90
c = 168.433	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		2022-08-23	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)	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	2.5	26.61	98.3	0.2	0.218	0.113	0.981	6.4	12.8		31086

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.58	87.1		0.56	0.61	0.898	2	9.7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.9	20.001	31086	1613	98.931	0.24	0.2383	0.2605	0.2793	0.3003	0.786

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]
-4.828			7.171		-2.343

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.353
r_dihedral_angle_6_deg	13.846
r_dihedral_angle_2_deg	10.192
r_lrange_it	8.94
r_lrange_other	8.756
r_dihedral_angle_1_deg	6.552
r_angle_refined_deg	1.485
r_angle_other_deg	0.514
r_rigid_bond_restr	0.454
r_nbd_refined	0.215
r_xyhbond_nbd_refined	0.203
r_symmetry_nbd_other	0.202
r_nbd_other	0.181
r_nbtor_refined	0.166
r_symmetry_xyhbond_nbd_refined	0.165
r_symmetry_nbd_refined	0.137
r_ncsr_local_group_4	0.119
r_ncsr_local_group_5	0.116
r_ncsr_local_group_2	0.115
r_ncsr_local_group_6	0.114
r_ncsr_local_group_1	0.111
r_symmetry_xyhbond_nbd_other	0.108
r_ncsr_local_group_3	0.101
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.074
r_metal_ion_refined	0.07
r_scangle_it	0.056
r_scangle_other	0.056
r_scbond_it	0.04
r_scbond_other	0.04
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9183
Nucleic Acid Atoms
Solvent Atoms	220
Heterogen Atoms	27

Software

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