7P2U | pdb_00007p2u

Crystal structure of Schistosoma mansoni HDAC8 in complex with a 3-chlorophenyl-spiroindoline capped hydroxamate-based inhibitor, bound to a novel site

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4BZ5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277.15	20-22% PEG 3350, 200mM sodium/potassium tartrate

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.369	α = 90
b = 70.369	β = 90
c = 186.346	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		2020-08-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.00	ELETTRA	11.2C

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	1.8	46.63	100	0.091	0.095	0.027	0.999	15	12.6		44460

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	1.8	1.84	99.3		3.534	3.693	1.06	0.498		11.9

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	4bz5	1.8	46.63	42160	2204	99.94	0.1808	0.179	0.19	0.2132	0.22	RANDOM	40.964

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]
1.35			1.35		-2.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.196
r_dihedral_angle_4_deg	21.49
r_dihedral_angle_3_deg	14.836
r_dihedral_angle_1_deg	5.934
r_angle_refined_deg	1.56
r_angle_other_deg	1.358
r_chiral_restr	0.084
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.196
r_dihedral_angle_4_deg	21.49
r_dihedral_angle_3_deg	14.836
r_dihedral_angle_1_deg	5.934
r_angle_refined_deg	1.56
r_angle_other_deg	1.358
r_chiral_restr	0.084
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3276
Nucleic Acid Atoms
Solvent Atoms	166
Heterogen Atoms	47

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.