9GN7 | pdb_00009gn7

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

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	12% (w/v) PEG 8000, 10% (v/v) glycerol and 0.5M KCl

Crystal Properties
Matthews coefficient	Solvent content
3.16	61.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 146.57	α = 90
b = 146.57	β = 90
c = 146.57	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	2019-10-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	1.0	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.18	47	100	0.997	10.8	1.7		27454		-3	39.05

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.18	2.25	99.9		0.832	2.5

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	2.18	46.393	27437	1378	99.978	0.15	0.1478	0.1476	0.1862	0.1847	43.205

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	16.486
r_dihedral_angle_3_deg	14.005
r_dihedral_angle_2_deg	11.793
r_lrange_other	10.202
r_lrange_it	10.172
r_scangle_it	9.272
r_scangle_other	9.27
r_scbond_it	7.262
r_scbond_other	7.262
r_dihedral_angle_1_deg	6.855
r_mcangle_it	6.392
r_mcangle_other	6.392
r_mcbond_it	4.944
r_mcbond_other	4.943
r_angle_refined_deg	2.236
r_angle_other_deg	0.756
r_nbd_refined	0.246
r_metal_ion_refined	0.21
r_symmetry_nbd_other	0.194
r_nbtor_refined	0.191
r_xyhbond_nbd_refined	0.183
r_nbd_other	0.139
r_symmetry_nbd_refined	0.113
r_chiral_restr	0.106
r_symmetry_nbtor_other	0.086
r_symmetry_xyhbond_nbd_refined	0.056
r_symmetry_xyhbond_nbd_other	0.039
r_bond_refined_d	0.014
r_gen_planes_refined	0.013
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	119
Heterogen Atoms	42

Software

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