9GN1 | pdb_00009gn1

Crystal structure of inactive Deacetylase (HdaH) H144A from Klebsiella pneumoniae subsp. ozaenae

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
3.13	60.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 146.117	α = 90
b = 146.117	β = 90
c = 146.117	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 PILATUS3 S 2M	mirror	2019-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.918400	BESSY	14.2

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	2.35	46.54	100	0.116	0.119	0.027	0.999	20.8	20		22209		-3	43.14

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	2.35	2.43	100		0.955	0.978	0.21	0.913	3.2	16.05

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	2.35	46.249	21754	1152	99.972	0.156	0.1533	0.1575	0.2042	0.2124	47.322

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	15.552
r_dihedral_angle_3_deg	14.893
r_dihedral_angle_2_deg	10.165
r_lrange_other	8.914
r_lrange_it	8.91
r_dihedral_angle_1_deg	7.7
r_scangle_it	7.392
r_scangle_other	7.302
r_mcangle_it	5.994
r_mcangle_other	5.993
r_scbond_it	5.59
r_scbond_other	5.505
r_mcbond_it	4.591
r_mcbond_other	4.567
r_angle_refined_deg	2.304
r_angle_other_deg	0.729
r_nbd_refined	0.26
r_metal_ion_refined	0.235
r_symmetry_nbd_other	0.196
r_nbtor_refined	0.188
r_xyhbond_nbd_refined	0.174
r_nbd_other	0.167
r_chiral_restr	0.095
r_symmetry_nbd_refined	0.094
r_symmetry_nbtor_other	0.087
r_symmetry_xyhbond_nbd_refined	0.046
r_bond_refined_d	0.013
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	2817
Nucleic Acid Atoms
Solvent Atoms	137
Heterogen Atoms	13

Software

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