6BOJ

Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	5.0mg/ml of PDE4D-UCR2 (CID7620) + 0.5mM BPN5004 against 8.75% w/v PEG1,000, 6.25% w/v PEG3,350, 6.25% w/v MPD, 0.015M NPS (sodium nitrate, disodium hydrogen phosphate, ammonium sulfate), 0.05M MOPS/HEPES-Na pH 7.5, 20% v/v ethanol, 0.05M Phosphate-citrate pH 4.2

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.78	α = 90
b = 81.89	β = 110.41
c = 116.79	γ = 90

Symmetry
Space Group	P 1 21 1

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	MARMOSAIC 300 mm CCD		2012-10-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	1.7	50	97.3	0.085	11.85	5.2		154546		-3	27.18

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	1.7	1.74	95.8		0.499	3	5.1

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	1.7	45.5	154544	7761	97.4	0.162	0.161	0.186	RANDOM	21.14

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]
0.27		-0.93	0.73		-0.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.372
r_dihedral_angle_4_deg	19.086
r_dihedral_angle_3_deg	12.949
r_dihedral_angle_1_deg	5.028
r_angle_refined_deg	1.408
r_angle_other_deg	1.216
r_chiral_restr	0.088
r_bond_refined_d	0.014
r_bond_other_d	0.008
r_gen_planes_refined	0.008
r_gen_planes_other	0.005
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	10567
Nucleic Acid Atoms
Solvent Atoms	1132
Heterogen Atoms	134

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
REFMAC	refinement