9K0H | pdb_00009k0h

The Crystal Structure of dsPETase05 from Biortus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2FX5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1M HEPES pH7.5, 25% PEG3,350

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.066	α = 90
b = 67.273	β = 96.529
c = 85.446	γ = 90

Symmetry
Space Group	P 1 21 1

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		2024-10-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL02U1	0.979191	SSRF	BL02U1

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	1.948	35.93	99.9	0.979	6.5	3.9		33866

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	1.948	2			0.801

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	1.948	35.924	33835	1708	99.644	0.151	0.1485	0.1604	0.1954	0.2077	12.763

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]
0.669		0.966	-1.354		0.452

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.049
r_dihedral_angle_3_deg	9.845
r_dihedral_angle_2_deg	8.057
r_dihedral_angle_1_deg	6.918
r_lrange_it	4.624
r_lrange_other	4.268
r_scangle_it	2.75
r_scangle_other	2.75
r_mcangle_other	2.086
r_mcangle_it	2.085
r_scbond_it	1.77
r_scbond_other	1.769
r_angle_refined_deg	1.539
r_mcbond_it	1.323
r_mcbond_other	1.296
r_angle_other_deg	0.539
r_nbd_refined	0.213
r_symmetry_nbd_other	0.209
r_symmetry_xyhbond_nbd_refined	0.205
r_xyhbond_nbd_refined	0.194
r_nbtor_refined	0.179
r_nbd_other	0.15
r_symmetry_xyhbond_nbd_other	0.142
r_symmetry_nbd_refined	0.111
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.073
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3794
Nucleic Acid Atoms
Solvent Atoms	523
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MoRDa	phasing