3G4L

Crystal structure of human phosphodiesterase 4d with roflumilast

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5	293	100MM HEPES PH 7.5, 35% ETHYLENE GLYCOL, 5% GLYCEROL, 22% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.665	α = 90
b = 111.952	β = 90
c = 161.701	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						SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1		ALS	5.0.1

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	2.5	50	99.4	0.11	5.4	6.6		63001

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)
	2.5	2.59	97.3		0.616		6

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.5	50	62929	3187		0.217	0.214	0.259	RANDOM	26.63

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]
-0.28			-0.19		0.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.752
r_dihedral_angle_4_deg	19.237
r_dihedral_angle_3_deg	16.051
r_dihedral_angle_1_deg	5.244
r_scangle_it	2.157
r_scbond_it	1.324
r_angle_refined_deg	1.278
r_angle_other_deg	1.009
r_mcangle_it	0.845
r_symmetry_vdw_refined	0.446
r_mcbond_it	0.436
r_symmetry_hbond_refined	0.254
r_symmetry_vdw_other	0.234
r_chiral_restr	0.158
r_xyhbond_nbd_refined	0.156
r_mcbond_other	0.142
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_gen_planes_other	0.006
r_bond_other_d	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10589
Nucleic Acid Atoms
Solvent Atoms	189
Heterogen Atoms	164

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement