5LI3 | pdb_00005li3

Crystal structure of HDAC-like protein from P. aeruginosa in complex with a photo-switchable inhibitor.

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, HANGING DROP	7.5	293	0.5M potassium hydrogen phosphate 0.5M sodium hydrogen phosphate 0.1M ammonium sulphate

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.19	α = 90
b = 82.19	β = 90
c = 217.03	γ = 90

Symmetry
Space Group	P 41 21 2

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		2015-09-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.0002	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.1	32	100	0.24	0.988	6.5	11.1		41043	2.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.16	100		0.92	0.84	2.5	11.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5g0x	2.4	32	28611	1424	99.96	0.22698	0.22473	0.23	0.27013	0.27	RANDOM	46.624

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]
1.44			1.44		-2.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.925
r_dihedral_angle_4_deg	15.919
r_dihedral_angle_3_deg	15.087
r_long_range_B_refined	6.333
r_long_range_B_other	6.319
r_dihedral_angle_1_deg	6.024
r_scangle_other	3.841
r_mcangle_it	3.368
r_mcangle_other	3.368
r_scbond_it	2.353
r_scbond_other	2.353
r_mcbond_it	2.065
r_mcbond_other	2.065
r_angle_refined_deg	1.391
r_angle_other_deg	1.111
r_chiral_restr	0.067
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5654
Nucleic Acid Atoms
Solvent Atoms	153
Heterogen Atoms	50

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing