1XOM

Catalytic Domain Of Human Phosphodiesterase 4D In Complex With Cilomilast

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	288	PEG3350, ethylene glycol, isopropanol, glycerol and DTT, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 288K

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.486	α = 90
b = 78.966	β = 90
c = 164.186	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	93	CCD	ADSC QUANTUM 210		2003-09-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.1	ALS	8.3.1

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	1.55	81.65	99.1	0.097	12.5	3.8	107956	107956

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)
	1.55	1.59	99.9		0.261	2.5	3.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	1.55	81.65	107956	107956	5683	99.08	0.18387	0.18276	0.24	0.20498	0.26	RANDOM	13.768

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]
0.23			-0.43		0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	2.667
r_scangle_it	2.516
r_scbond_it	1.515
r_angle_refined_deg	1.093
r_mcangle_it	0.939
r_angle_other_deg	0.782
r_mcbond_it	0.475
r_symmetry_vdw_other	0.293
r_nbd_other	0.219
r_nbd_refined	0.204
r_xyhbond_nbd_refined	0.117
r_symmetry_hbond_refined	0.113
r_symmetry_vdw_refined	0.088
r_nbtor_other	0.08
r_chiral_restr	0.07
r_bond_refined_d	0.006
r_gen_planes_refined	0.004
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5288
Nucleic Acid Atoms
Solvent Atoms	596
Heterogen Atoms	184

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
ELVES	data scaling
EPMR	phasing