9H4U | pdb_00009h4u

Deacetylase FI8 utilizes unconventional variant of a catalytic triad: the diluted triad

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold		AlphaFold2 model with the correct sequence

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	Crystallization condition: 0.3 uL protein solution (9.3 mg/mL protein) and 0.3 uL well solution (0.2 M Ca-acetate, 0.1 M Na-cacodylate pH 6.5, 18% PEG8000). Cryo condition: 0.2 M Ca-acetate, 0.1 M Na-cacodylate, 22% PEG8000, 8% PEG400.

Crystal Properties
Matthews coefficient	Solvent content
2.85	57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.663	α = 90
b = 120.04	β = 90
c = 141.548	γ = 90

Symmetry
Space Group	P 21 21 21

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		2022-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9763	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim 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	1.54	50	96.5	0.103	0.107	0.998	12.6	12.5		2930895		-3	31.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.54	1.63	78.4		2.07	2.19	0.396	0.78	9

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	1.541	48.378	232111	11957	95.955	0.171	0.1697	0.1763	0.2009	0.2067	30.865

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]
-0.956			1.331		-0.374

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.081
r_dihedral_angle_3_deg	12.833
r_dihedral_angle_2_deg	8.995
r_lrange_it	7.675
r_lrange_other	7.576
r_dihedral_angle_1_deg	6.979
r_scangle_it	6.063
r_scangle_other	6.063
r_scbond_it	3.959
r_scbond_other	3.959
r_mcangle_it	3.283
r_mcangle_other	3.283
r_mcbond_it	2.369
r_mcbond_other	2.369
r_angle_refined_deg	1.813
r_angle_other_deg	0.634
r_nbd_other	0.263
r_symmetry_nbd_refined	0.259
r_nbd_refined	0.218
r_symmetry_nbd_other	0.194
r_nbtor_refined	0.184
r_metal_ion_refined	0.17
r_symmetry_xyhbond_nbd_refined	0.166
r_xyhbond_nbd_refined	0.158
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9932
Nucleic Acid Atoms
Solvent Atoms	1095
Heterogen Atoms	111

Software

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