7QJO

Crystal structure of a cutinase enzyme from Marinactinospora thermotolerans DSM45154 (606)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M Sodium HEPES pH 7.5, 70% (v/v) MPD

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.966	α = 90
b = 45.354	β = 108.193
c = 86.598	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		2021-07-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	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	1.933	82.269	91.6	0.253	0.114	0.988	5.5	5.9		29683

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	1.933	2.097	52		1.343	0.555	0.577	1.4	6.7

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4WFJ	1.933	82.269	29683	1448	71.91	0.235	0.2322	0.282	18.851

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]
-0.485		0.121	-0.195		0.494

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.569
r_dihedral_angle_4_deg	17.485
r_dihedral_angle_3_deg	14.575
r_dihedral_angle_1_deg	7.343
r_lrange_it	2.858
r_lrange_other	2.791
r_angle_refined_deg	1.74
r_angle_other_deg	1.342
r_scangle_it	1.205
r_scangle_other	1.204
r_mcangle_other	1.156
r_mcangle_it	1.155
r_scbond_it	0.726
r_scbond_other	0.726
r_mcbond_it	0.682
r_mcbond_other	0.675
r_nbd_other	0.359
r_symmetry_nbd_refined	0.298
r_xyhbond_nbd_refined	0.216
r_nbd_refined	0.208
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.17
r_symmetry_xyhbond_nbd_refined	0.158
r_symmetry_xyhbond_nbd_other	0.106
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.077
r_ncsr_local_group_1	0.053
r_bond_refined_d	0.011
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	4044
Nucleic Acid Atoms
Solvent Atoms	248
Heterogen Atoms

Software

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