2GH6 | pdb_00002gh6

Crystal structure of a HDAC-like protein with 9,9,9-trifluoro-8-oxo-N-phenylnonan amide bound

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZZ1	PDB ENTRY 1ZZ1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	NaCl, Na-cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.507	α = 90
b = 94.897	β = 104.28
c = 123.301	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		IMAGE PLATE	RIGAKU			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.203	39.84				76561	76561

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.203	2.26	92.9

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 (All)	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	PDB ENTRY 1ZZ1	2.203	39.84	72678	3863	98.91	0.16082	0.16082	0.15797	0.16	0.21419	0.21	RANDOM	24.778

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]
0.01			0.01		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.493
r_dihedral_angle_4_deg	18.06
r_dihedral_angle_3_deg	14.534
r_dihedral_angle_1_deg	6.564
r_scangle_it	3.491
r_scbond_it	2.225
r_angle_refined_deg	1.559
r_mcangle_it	1.184
r_mcbond_it	0.651
r_nbtor_refined	0.299

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.493
r_dihedral_angle_4_deg	18.06
r_dihedral_angle_3_deg	14.534
r_dihedral_angle_1_deg	6.564
r_scangle_it	3.491
r_scbond_it	2.225
r_angle_refined_deg	1.559
r_mcangle_it	1.184
r_mcbond_it	0.651
r_nbtor_refined	0.299
r_metal_ion_refined	0.242
r_nbd_refined	0.22
r_symmetry_vdw_refined	0.159
r_xyhbond_nbd_refined	0.146
r_chiral_restr	0.102
r_symmetry_hbond_refined	0.1
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10988
Nucleic Acid Atoms
Solvent Atoms	783
Heterogen Atoms	96

Software

Software
Software Name	Purpose
HKL-2000	data reduction
MOLREP	phasing
REFMAC	refinement
HKL-2000	data scaling

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.