5K1I

PDE4 crystal structure in complex with small molecule inhibitor

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	293	19% PEG 3350, 36 % Ethylene Glycol and 10 % Isopropanol as a precipitant

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.444	α = 91.01
b = 78.347	β = 92.79
c = 161.756	γ = 90.08

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	IMAGE PLATE	MARRESEARCH		2005-04-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ENRAF-NONIUS FR571	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	2.6	25	94.6	0.126	7	2.6		91922	7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.74			0.395

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	1TB7	2.61	25	82704	4409	94.77	0.1947	0.1913	0.2583	RANDOM	30.959

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]
-0.01	0.18	0.37	0.15	-0.55	-0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.423
r_dihedral_angle_3_deg	17.812
r_dihedral_angle_4_deg	15.917
r_dihedral_angle_1_deg	5.525
r_angle_refined_deg	1.471
r_scangle_it	1.087
r_mcangle_it	1.05
r_scbond_it	0.718
r_mcbond_it	0.66
r_nbtor_refined	0.328

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.423
r_dihedral_angle_3_deg	17.812
r_dihedral_angle_4_deg	15.917
r_dihedral_angle_1_deg	5.525
r_angle_refined_deg	1.471
r_scangle_it	1.087
r_mcangle_it	1.05
r_scbond_it	0.718
r_mcbond_it	0.66
r_nbtor_refined	0.328
r_symmetry_hbond_refined	0.265
r_nbd_refined	0.257
r_symmetry_vdw_refined	0.243
r_xyhbond_nbd_refined	0.188
r_chiral_restr	0.1
r_metal_ion_refined	0.089
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20993
Nucleic Acid Atoms
Solvent Atoms	210
Heterogen Atoms	240

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.