9HYD | pdb_00009hyd

PETaseSM14 from marine-sponge Streptomyces sp.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-A0A679PDB4-F1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	0.2 M Ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 30% w/v Polyethylene glycol monomethyl ether 5,000

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.983	α = 90
b = 96.983	β = 90
c = 44.815	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 EIGER2 XE 16M		2024-01-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.7133	Diamond	I03

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	1.425	83.99	100	0.999	8.9	21.3		45062

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	1.425	1.45			0.305

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	NONE	1.425	83.99	45061	2279	99.971	0.14	0.1363	0.1397	0.2018	0.2042	22.788

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]
0.167	0.084		0.167		-0.543

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.515
r_dihedral_angle_3_deg	13.218
r_dihedral_angle_2_deg	10.196
r_dihedral_angle_1_deg	6.789
r_lrange_it	6.108
r_rigid_bond_restr	5.932
r_scangle_it	5.827
r_scangle_other	5.825
r_scbond_it	5.697
r_scbond_other	5.695
r_lrange_other	5.264
r_mcangle_it	3.296
r_mcangle_other	3.295
r_mcbond_it	3.051
r_mcbond_other	3.043
r_angle_refined_deg	1.623
r_angle_other_deg	0.575
r_symmetry_nbd_refined	0.275
r_nbd_refined	0.232
r_nbd_other	0.221
r_xyhbond_nbd_refined	0.211
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.152
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.079
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1994
Nucleic Acid Atoms
Solvent Atoms	296
Heterogen Atoms	30

Software

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