8C65 | pdb_00008c65

Crystal structure of cutinase AdCut from Acidovorax delafieldii (PBS depolymerase)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold		AF2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	20 % PEG 3350, 0.2 M ammonium citrate dibasic

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.798	α = 90
b = 96.43	β = 111.033
c = 58.525	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 EIGER2 XE 16M		2022-01-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim 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	1.491	54.626	78.1	0.195	0.08	0.995	7.1	6.7		39403

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.491	1.594	65.5		1.262	0.508	0.529	1.5	7

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	1.491	54.626	39402	1897	51.098	0.177	0.1753	0.19	0.2147	0.22	10.792

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]
0.17		0.092	0.047		-0.222

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.632
r_dihedral_angle_3_deg	12.922
r_dihedral_angle_2_deg	8.239
r_dihedral_angle_1_deg	7.082
r_lrange_it	3.854
r_lrange_other	3.722
r_scangle_it	1.743
r_scangle_other	1.742
r_angle_refined_deg	1.518
r_mcangle_other	1.364
r_mcangle_it	1.36
r_scbond_it	1.109
r_scbond_other	1.105
r_mcbond_it	0.796
r_mcbond_other	0.792
r_angle_other_deg	0.549
r_xyhbond_nbd_refined	0.238
r_nbd_refined	0.225
r_symmetry_xyhbond_nbd_refined	0.224
r_symmetry_nbd_refined	0.211
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.18
r_nbd_other	0.165
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.077
r_ncsr_local_group_1	0.068
r_bond_refined_d	0.009
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	3976
Nucleic Acid Atoms
Solvent Atoms	405
Heterogen Atoms

Software

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