3D3P

Crystal structure of PDE4B catalytic domain in complex with a pyrazolopyridine inhibitor

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	14-18% PEG 3000, 10% Glycerol, 50mM Sodium Cacodylate pH 6.5, 100mM Sodium Acetate, 1M Sodium Chloride, 1% DMF, 5mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.448	α = 90
b = 94.725	β = 90
c = 105.671	γ = 90

Symmetry
Space Group	I 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 4		2002-10-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.9326	ESRF	ID14-4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.75	25	98.4	0.062	10.9			44609			23.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.75	1.81	97.4		0.451	2.5		4351

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	PDB ENTRY 1F0J (Molecule A)	1.75	20	44290	2235	100	0.201	0.199	0.241	RANDOM	30.138

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]
-1.87			-0.36		2.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.192
r_dihedral_angle_4_deg	26.357
r_dihedral_angle_3_deg	14.419
r_scangle_it	5.109
r_dihedral_angle_1_deg	4.926
r_scbond_it	3.605
r_mcangle_it	2.811
r_mcbond_it	2.047
r_angle_refined_deg	1.363
r_nbtor_refined	0.306

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.192
r_dihedral_angle_4_deg	26.357
r_dihedral_angle_3_deg	14.419
r_scangle_it	5.109
r_dihedral_angle_1_deg	4.926
r_scbond_it	3.605
r_mcangle_it	2.811
r_mcbond_it	2.047
r_angle_refined_deg	1.363
r_nbtor_refined	0.306
r_nbd_refined	0.218
r_xyhbond_nbd_refined	0.179
r_symmetry_vdw_refined	0.177
r_symmetry_hbond_refined	0.149
r_chiral_restr	0.097
r_metal_ion_refined	0.026
r_bond_refined_d	0.015
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2714
Nucleic Acid Atoms
Solvent Atoms	303
Heterogen Atoms	34

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
AMoRE	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.