8ZHY | pdb_00008zhy

Magnesium substituted Terephthalate 1,2-cis-dihydrodioldehydrogenase/Decarboxylase in complex with CO2.

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 TacsimateTM pH 6.0 12% w/v Polyethylene glycol 3,350

Crystal Properties
Matthews coefficient	Solvent content
2.56	52.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.729	α = 90
b = 93.776	β = 90
c = 166.309	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		2022-11-23	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	2.7	26.22	99.6	0.1	0.25	0.094	0.969	6.2	6.7		42297

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	2.7	9.73	100		0.64	0.685	0.241	0.785	2.6

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	2.7	20.001	37748	1855	99.217	0.285	0.2829	0.2844	0.3303	0.3324	31.117

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]
-2.756			2.567		0.189

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.4
r_dihedral_angle_6_deg	13.105
r_dihedral_angle_2_deg	6.901
r_dihedral_angle_1_deg	6.666
r_angle_refined_deg	1.3
r_angle_other_deg	0.446
r_nbd_refined	0.224
r_symmetry_nbd_other	0.194
r_nbd_other	0.177
r_symmetry_xyhbond_nbd_refined	0.168
r_nbtor_refined	0.165
r_xyhbond_nbd_refined	0.162
r_symmetry_nbd_refined	0.153
r_ncsr_local_group_3	0.081
r_ncsr_local_group_4	0.081
r_ncsr_local_group_6	0.081
r_ncsr_local_group_1	0.078
r_ncsr_local_group_2	0.078
r_symmetry_nbtor_other	0.077
r_ncsr_local_group_5	0.076
r_chiral_restr	0.062
r_bond_refined_d	0.006
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9148
Nucleic Acid Atoms
Solvent Atoms	153
Heterogen Atoms	32

Software

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