Experiment: 5WH5

Crystal structure of the PDE4D2 catalytic domain in complex with inhibitor (R)-Zl-n-91

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	7.5	277	The ~10mg/ml PDE4D2 (86-413) was stored in a buffer of 20 mM Tris.base, pH 7.5, 50 mM NaCl, 1 mM 2-mercaptoethanol, 1 mM EDTA and mixed with 2 mM (R)- or (S)-5. They were crystallized at 4C by hanging drop against a well buffer of 0.1 M HEPES pH 7.5, 15% PEG3350, 30% ethylene glycol, and 10% isopropanol.

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.467	α = 90
b = 79.883	β = 90
c = 163.444	γ = 90

Symmetry
Space Group	P 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	Bruker AXIOM 200		2008-04-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.0	NSLS	X29A

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	1.8	81.72	94.6	8.8	13.2		69331

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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		THROUGHOUT	1.8	30	65854	3389	94.17	0.1941	0.1931	0.2018	0.2141	0.2197	RANDOM	26.926

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]
-0.02					0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.117
r_dihedral_angle_4_deg	11.835
r_dihedral_angle_3_deg	11.495
r_dihedral_angle_1_deg	4.369
r_angle_refined_deg	0.952
r_angle_other_deg	0.744
r_chiral_restr	0.054
r_bond_refined_d	0.005
r_gen_planes_refined	0.003
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.117
r_dihedral_angle_4_deg	11.835
r_dihedral_angle_3_deg	11.495
r_dihedral_angle_1_deg	4.369
r_angle_refined_deg	0.952
r_angle_other_deg	0.744
r_chiral_restr	0.054
r_bond_refined_d	0.005
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5271
Nucleic Acid Atoms
Solvent Atoms	388
Heterogen Atoms	49

Software

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