7K4O

Tannin acyl hydrolase from Aspergillus niger

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3WMT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	281	zinc sulfate, polyethylene glycol monomethyl ether 500 and 0.1 M sodium MES at pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
3.85	68.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 170.92	α = 90
b = 170.92	β = 90
c = 111.061	γ = 120

Symmetry
Space Group	P 65 2 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 EIGER X 16M		2019-03-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.9792	Australian Synchrotron	MX2

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	1.65	19.76	99.9	0.079	0.023	0.999	20.9	13.4		114035

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	1.65	1.71			1.396	0.384	0.689	1.8

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	3wmt	1.65	19.76	114035	5698	99.897	0.153	0.1521	0.1738	30.724

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]
-0.272	-0.136		-0.272		0.881

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.105
r_dihedral_angle_4_deg	19.133
r_dihedral_angle_3_deg	11.745
r_lrange_it	6.792
r_lrange_other	6.487
r_dihedral_angle_1_deg	6.247
r_scangle_other	5.593
r_scangle_it	5.469
r_scbond_other	3.9
r_scbond_it	3.683
r_mcangle_it	3.464
r_mcangle_other	3.464
r_angle_other_deg	3.165
r_mcbond_it	2.562
r_mcbond_other	2.562
r_angle_refined_deg	1.88
r_xyhbond_nbd_refined	0.232
r_nbd_refined	0.219
r_symmetry_nbd_other	0.214
r_symmetry_nbd_refined	0.212
r_nbd_other	0.187
r_nbtor_refined	0.178
r_symmetry_xyhbond_nbd_refined	0.146
r_metal_ion_refined	0.123
r_symmetry_metal_ion_refined	0.112
r_symmetry_nbtor_other	0.104
r_chiral_restr	0.096
r_bond_other_d	0.035
r_gen_planes_other	0.019
r_bond_refined_d	0.014
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4280
Nucleic Acid Atoms
Solvent Atoms	775
Heterogen Atoms	337

Software

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