6QGC

PETase from Ideonella sakaiensis without ligand

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4CG1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	293	1 ul protein (10 mg/ml, 20 mM TRIS pH 7.5, 150 mM NaCl) + 1 ul reservoir (0.1 M sodium citrate or sodium acetate pH 5.0, 15% (v/v) PEG8000, 0.5 M lithium sulfate)

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.121	α = 90
b = 78.769	β = 92.56
c = 140.121	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 PILATUS 6M	mirror	2017-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9799	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim 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	100	97.1	0.131	0.151	0.991	8.4	4.2		73090			27.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.12	95.3		0.719	0.838	0.62	1.6	3.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4CG1	2	48.73	69684	3607	97.43	0.21578	0.21347	0.26091	RANDOM	23.386

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]
1.3		0.33	-2.11		0.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.802
r_dihedral_angle_4_deg	17.402
r_dihedral_angle_3_deg	13.874
r_dihedral_angle_1_deg	7.406
r_long_range_B_refined	4.467
r_long_range_B_other	4.401
r_angle_refined_deg	1.817
r_angle_other_deg	1.052
r_scangle_other	0.826
r_mcangle_it	0.658
r_mcangle_other	0.658
r_scbond_it	0.587
r_scbond_other	0.517
r_mcbond_it	0.385
r_mcbond_other	0.385
r_chiral_restr	0.086
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001
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	7689
Nucleic Acid Atoms
Solvent Atoms	454
Heterogen Atoms	19

Software

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