9GKV

Crystal Structure of Deacetylase (HdaH) from Vibrio cholerae in complex with SAHA

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-A0A395TF31-F1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	1.4 M sodium acetate 0.1 M MES pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.92	α = 90
b = 81.53	β = 90
c = 133.17	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 PILATUS 6M	mirror	2024-04-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.9	47.607	96.9	0.105	0.11	0.999	12.7	11.3		43149

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.9	1.94	81.1		0.756	0.825	0.318	0.911	1.7	5.9

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.9	47.607	43053	2162	96.644	0.178	0.175	0.2403	29.447

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]
2.756			0.404		-3.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	15.605
r_dihedral_angle_6_deg	15.092
r_dihedral_angle_3_deg	13.703
r_lrange_it	8.693
r_lrange_other	8.635
r_dihedral_angle_1_deg	6.973
r_scangle_it	6.278
r_scangle_other	6.277
r_mcangle_other	4.42
r_mcangle_it	4.415
r_scbond_it	4.385
r_scbond_other	4.384
r_mcbond_it	3.213
r_mcbond_other	3.173
r_angle_refined_deg	2.09
r_angle_other_deg	0.719
r_metal_ion_refined	0.28
r_nbd_refined	0.265
r_symmetry_xyhbond_nbd_refined	0.264
r_symmetry_nbd_refined	0.235
r_nbd_other	0.223
r_symmetry_xyhbond_nbd_other	0.221
r_xyhbond_nbd_refined	0.216
r_symmetry_nbd_other	0.199
r_nbtor_refined	0.183
r_chiral_restr	0.101
r_symmetry_nbtor_other	0.085
r_ncsr_local_group_1	0.071
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4817
Nucleic Acid Atoms
Solvent Atoms	363
Heterogen Atoms	37

Software

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