6THT | pdb_00006tht

High resolution crystal structure of a Leaf-branch compost cutinase quintuple variant

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4EB0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8	285	0.1 M Imidazole, 1 M Sodium Citrate

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.413	α = 90
b = 109.413	β = 90
c = 35.183	γ = 120

Symmetry
Space Group	P 63

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		2018-07-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.97625	ESRF	ID30B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	1.14	94.75	100	0.102	11.2	9.5		87457

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	1.14	1.16	100		1.051	0.364	0.744	2.1	9.2

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4EB0	1.14	94.75	83089	4368	99.99	0.1143	0.1132	0.11	0.1365	0.14	RANDOM	15.815

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]
-0.06	-0.03		-0.06		0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_bonded	32.087
r_dihedral_angle_2_deg	28.409
r_dihedral_angle_1_deg	24.794
r_sphericity_free	21.226
r_dihedral_angle_4_deg	17.43
r_dihedral_angle_3_deg	9.403
r_rigid_bond_restr	7.486
r_angle_refined_deg	1.844
r_angle_other_deg	1.213
r_chiral_restr	0.138

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_bonded	32.087
r_dihedral_angle_2_deg	28.409
r_dihedral_angle_1_deg	24.794
r_sphericity_free	21.226
r_dihedral_angle_4_deg	17.43
r_dihedral_angle_3_deg	9.403
r_rigid_bond_restr	7.486
r_angle_refined_deg	1.844
r_angle_other_deg	1.213
r_chiral_restr	0.138
r_bond_refined_d	0.019
r_gen_planes_refined	0.012
r_bond_other_d	0.004
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1948
Nucleic Acid Atoms
Solvent Atoms	299
Heterogen Atoms	24

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.