3O56

Catalytic domain of human phosphodiesterase 4b2b in complex with a 5-heterocycle pyrazolopyridine inhibitor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3D3P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	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 277K

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.531	α = 90
b = 94.592	β = 90
c = 105.089	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		2004-02-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.9393	ESRF	ID14-4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.42	29.703	99.6	0.094	0.094	16.5	7.2		17117			52.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.42	2.48	100		0.379	0.379	2	7.3	1253

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	FOURIER SYNTHESIS	THROUGHOUT	3D3P	2.42	20	17097	865	100	0.1993	0.1962	0.2601	RANDOM	57.0208

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]
-6.19			-3.21		9.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.595
r_dihedral_angle_3_deg	16.163
r_dihedral_angle_4_deg	15.043
r_scangle_it	5.611
r_dihedral_angle_1_deg	4.937
r_scbond_it	3.722
r_mcangle_it	3.066
r_mcbond_it	1.741
r_angle_refined_deg	1.325
r_angle_other_deg	0.905

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.595
r_dihedral_angle_3_deg	16.163
r_dihedral_angle_4_deg	15.043
r_scangle_it	5.611
r_dihedral_angle_1_deg	4.937
r_scbond_it	3.722
r_mcangle_it	3.066
r_mcbond_it	1.741
r_angle_refined_deg	1.325
r_angle_other_deg	0.905
r_mcbond_other	0.464
r_chiral_restr	0.078
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2705
Nucleic Acid Atoms
Solvent Atoms	124
Heterogen Atoms	48

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
REFMAC	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.