8YMA | pdb_00008yma

CRYSTAL STRUCTURE OF A NOVEL PU PLASTIC DEGRADATION ENZYME FROM THERMAEROBACTER MARIANENSIS

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	298	1.0M (NH4)2HPO4, 0.1M imidazole pH 8.0, 0.2M NaCl

Crystal Properties
Matthews coefficient	Solvent content
3.03	59.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.834	α = 90
b = 81.834	β = 90
c = 667.371	γ = 120

Symmetry
Space Group	P 61

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 EIGER X 16M		2023-09-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL10U2	0.9792	SSRF	BL10U2

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	2.07	48.59	99.9	0.995	11.8	21.5		153365

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	2.07	2.1			0.643		21.3

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.07	48.59	145412	7698	99.88	0.184	0.18171	0.1958	0.22742	0.2306	RANDOM	48.772

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]
11.84			11.84		-23.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.607
r_long_range_B_refined	12.901
r_long_range_B_other	12.897
r_dihedral_angle_2_deg	11.86
r_mcangle_it	8.718
r_mcangle_other	8.718
r_scangle_other	8.1
r_dihedral_angle_1_deg	6.491
r_mcbond_it	6.407
r_mcbond_other	6.407
r_scbond_it	5.964
r_scbond_other	5.962
r_angle_refined_deg	1.51
r_angle_other_deg	0.523
r_chiral_restr	0.073
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
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	14893
Nucleic Acid Atoms
Solvent Atoms	481
Heterogen Atoms	5

Software

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