8VE9 | pdb_00008ve9

IsPETase - ACCCETN mutant - CombiPETase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		unpublished in-house structure solved using PDB entry 6EQE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	3.71	293	22.4% (w/v) PEG 3350, 0.23 M TMAO, 0.1 M trisodium citrate-citric acid pH 3.71

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.475	α = 90
b = 68.259	β = 90
c = 78.592	γ = 90

Symmetry
Space Group	P 21 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	DECTRIS EIGER X 16M		2023-11-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.95373	Australian Synchrotron	MX2

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	1.6	51.588	99.8	0.999	14.7	13.5		36462

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	1.6	1.6			0.972

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	1.6	51.588	36462	1823	99.765	0.146	0.145	0.16	0.1717	0.18	21.262

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]
-1.071			0.11		0.962

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.025
r_dihedral_angle_3_deg	11.285
r_dihedral_angle_2_deg	10.624
r_dihedral_angle_1_deg	6.576
r_lrange_it	5
r_lrange_other	4.826
r_scangle_it	3.999
r_scangle_other	3.998
r_scbond_it	2.751
r_scbond_other	2.749
r_mcangle_it	2.419
r_mcangle_other	2.418
r_mcbond_other	1.853
r_mcbond_it	1.849
r_angle_refined_deg	1.846
r_angle_other_deg	0.648
r_xyhbond_nbd_refined	0.25
r_nbd_refined	0.22
r_symmetry_nbd_other	0.201
r_nbd_other	0.195
r_nbtor_refined	0.181
r_symmetry_nbd_refined	0.169
r_symmetry_xyhbond_nbd_refined	0.132
r_chiral_restr	0.099
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1928
Nucleic Acid Atoms
Solvent Atoms	197
Heterogen Atoms	13

Software

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