9GN6

Crystal Structure of Deacetylase (HdaH) from Klebsiella pneumoniae subsp. ozaenae in complex with the inhibitor SAHA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5G0X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	2% (w/v) PEG 8000, 10% (v/v) glycerol and 0.5M KCl

Crystal Properties
Matthews coefficient	Solvent content
3.13	60.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 146.206	α = 90
b = 146.206	β = 90
c = 146.206	γ = 90

Symmetry
Space Group	I 2 3

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	mirror	2019-10-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	1.000000	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.95	46.3	100	0.02	0.028	0.02	1	16.3	1.9		37885		-3	41.09

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2	100		0.844	0.597	0.532	1.3	2

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	1.95	46.277	37871	1859	99.989	0.139	0.1373	0.1387	0.1756	0.1784	48.525

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.891
r_dihedral_angle_3_deg	13.017
r_dihedral_angle_2_deg	9.305
r_lrange_it	8.753
r_lrange_other	8.639
r_dihedral_angle_1_deg	6.455
r_scangle_it	6.383
r_scangle_other	6.382
r_scbond_it	4.598
r_scbond_other	4.596
r_mcangle_it	4.457
r_mcangle_other	4.456
r_mcbond_it	3.392
r_mcbond_other	3.39
r_angle_refined_deg	1.962
r_angle_other_deg	0.647
r_metal_ion_refined	0.254
r_xyhbond_nbd_refined	0.239
r_nbd_refined	0.238
r_symmetry_nbd_other	0.188
r_nbtor_refined	0.185
r_nbd_other	0.145
r_symmetry_nbd_refined	0.12
r_symmetry_xyhbond_nbd_refined	0.107
r_chiral_restr	0.093
r_symmetry_nbtor_other	0.082
r_symmetry_xyhbond_nbd_other	0.036
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2822
Nucleic Acid Atoms
Solvent Atoms	232
Heterogen Atoms	22

Software

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