5OHJ

Human phosphodiesterase 4B catalytic domain in complex with a pyrrolidinyl inhibitor.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		dimer of the catalytic domain of PDE4D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	293	Drops comprised 2microliters protein solution mixed with reservoir buffer consisting of 100mM sodium acetate pH 4.5, 14% PEG400 and 50mM calcium acetate. After 2 days they were streak seeded with crystals obtained from rolipram complex seed stock. Crystals, up to 100 microns in largest dimension, grew from precipitate after 1-2 weeks. Crystals were transferred to a cryoprotectant solution (100mM sodium acetate pH 4.5, 14% PEG400, 50mM calcium acetate and 20% glycerol) then flash-frozen prior to X-ray data collection.

Crystal Properties
Matthews coefficient	Solvent content
1.8	31.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.27	α = 90
b = 55.73	β = 90
c = 225.56	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	PIXEL	DECTRIS PILATUS 2M		2012-10-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.51	29.61	77.7	0.046	0.041	0.999	22.4	6.4		85681

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.51	1.55	28.3		0.467	0.149	0.791	2.6	3.7

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	MOLECULAR REPLACEMENT	THROUGHOUT	dimer of the catalytic domain of PDE4D	1.6	29.61	76169	4027	86.14	0.18549	0.1841	0.21153	RANDOM	22.688

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]
-0.18			0.4		-0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.507
r_dihedral_angle_4_deg	21.02
r_dihedral_angle_3_deg	15.7
r_dihedral_angle_1_deg	5.809
r_angle_refined_deg	1.88
r_chiral_restr	0.131
r_bond_refined_d	0.019
r_gen_planes_refined	0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5421
Nucleic Acid Atoms
Solvent Atoms	165
Heterogen Atoms	100

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing