9QYT | pdb_00009qyt

Crystal structure of leaf branch compost cutinase variant ICCG L50Y T110E

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6THT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		293	10 mM Tris, 150 mM NaCl, 0.6 M succinic acid, pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
3.19	61.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.21	α = 90
b = 97.21	β = 90
c = 74.67	γ = 90

Symmetry
Space Group	P 41 21 2

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 PILATUS3 6M		2024-07-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.000	PETRA III, DESY	P11

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	1.64	48.605	98.5	0.999	15.98	26.18		1147084

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	1.64	1.74			0.517

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	1.64	48.605	43749	2188	98.596	0.204	0.2031	0.203	0.2277	0.2277	33.757

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]
-0.855			-0.855		1.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.868
r_dihedral_angle_3_deg	11.33
r_dihedral_angle_2_deg	7.775
r_dihedral_angle_1_deg	6.978
r_lrange_it	6.257
r_scangle_it	4.736
r_scbond_it	3.716
r_mcangle_it	3.639
r_mcbond_it	2.992
r_angle_refined_deg	1.933
r_nbtor_refined	0.312
r_metal_ion_refined	0.29
r_nbd_refined	0.218
r_symmetry_nbd_refined	0.208
r_xyhbond_nbd_refined	0.203
r_symmetry_xyhbond_nbd_refined	0.128
r_chiral_restr	0.124
r_bond_refined_d	0.01
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1945
Nucleic Acid Atoms
Solvent Atoms	236
Heterogen Atoms	9

Software

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