6ZBA

Crystal structure of PDE4D2 in complex with inhibitor LEO39652

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	Protein stored at 20.6 mg/mL in a storage buffer of 50 mM NaCl, 20 mM Tris HCl (pH 7.5), 1 mM TCEP, 1 mM EDTA. Reservoir was 0.1 M HEPES (pH 7.5), 19% PEG3350, 25% ethylene glycol, 5% 2-propanol, 5% glycerol. Drops were microseeded. Apo crystals were soaked with 0.8 mM LEO39652A for 3 days.

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.03	α = 90
b = 111.866	β = 90
c = 159.623	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 EIGER2 X 9M		2019-09-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9159	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.6	79.939	100	0.085	0.997	9.2	6.6		235229

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.63	100		1.481	0.422	1	6

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-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1Y2K	1.6	79.939	235038	11947	99.938	0.163	0.1616	0.1918	27.135

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]
0.009			-0.008		-0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.745
r_dihedral_angle_4_deg	16.941
r_dihedral_angle_3_deg	13.454
r_lrange_it	6.874
r_lrange_other	6.455
r_dihedral_angle_1_deg	5.423
r_scangle_it	4.972
r_scangle_other	4.971
r_scbond_it	3.319
r_scbond_other	3.319
r_mcangle_it	2.804
r_mcangle_other	2.804
r_mcbond_it	2.157
r_mcbond_other	2.157
r_angle_refined_deg	1.59
r_angle_other_deg	1.521
r_nbd_other	0.243
r_xyhbond_nbd_refined	0.242
r_symmetry_xyhbond_nbd_refined	0.233
r_nbd_refined	0.231
r_symmetry_nbd_refined	0.217
r_symmetry_nbd_other	0.18
r_nbtor_refined	0.169
r_symmetry_xyhbond_nbd_other	0.136
r_chiral_restr	0.09
r_symmetry_nbtor_other	0.082
r_metal_ion_refined	0.024
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10650
Nucleic Acid Atoms
Solvent Atoms	1344
Heterogen Atoms	260

Software

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