9QYU | pdb_00009qyu

Crystal structure of leaf branch compost cutinase quintuple variant ICCG L50Y

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
3.12	60.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.65	α = 90
b = 96.65	β = 90
c = 73.71	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 PILATUS 6M		2023-08-14	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	1.51	48.56	100	1	25.82	19.88		1098150

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	1.51	1.6			0.678

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	1.51	48.325	55242	2763	99.987	0.151	0.1494	0.1941	0.1836	0.1919	33.521

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]
1.121			1.121		-2.243

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.274
r_lrange_it	15.378
r_scangle_it	11.835
r_dihedral_angle_3_deg	10.787
r_scbond_it	9.363
r_mcangle_it	8.809
r_dihedral_angle_2_deg	8.004
r_dihedral_angle_1_deg	6.635
r_mcbond_it	6.625
r_rigid_bond_restr	5.078
r_angle_refined_deg	1.59
r_nbtor_refined	0.309
r_nbd_refined	0.211
r_symmetry_nbd_refined	0.206
r_symmetry_xyhbond_nbd_refined	0.12
r_xyhbond_nbd_refined	0.118
r_chiral_restr	0.105
r_bond_refined_d	0.01
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1943
Nucleic Acid Atoms
Solvent Atoms	205
Heterogen Atoms	25

Software

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