3ITU | pdb_00003itu

hPDE2A catalytic domain complexed with IBMX

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	Reservoir: 25% PEG 3350, 0.1M Tris pH8.5, 0.2M MgCl2 Protein: 25mM HEPES pH 7.5, 25mM NaCl, 2mM TCEP, 10ug/ml E-64, 1ug/ml pepstatin, 1mM IBMX, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.815	α = 109.3
b = 73.287	β = 88.8
c = 91.532	γ = 89

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	100	CCD	ADSC QUANTUM 315			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.00	APS	23-ID-B

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	1.58	50	83.9	0.11	8.8	2.7		157174		-3

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)
	1.58	1.64	36.7		0.338		1.2	6904

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.58	50	157107	7854	83.76	0.177	0.174	0.17	0.233	0.23	RANDOM	22.692

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]
-0.04	0.03	0.75	-0.23	-0.07	0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.976
r_dihedral_angle_4_deg	17.766
r_dihedral_angle_3_deg	14.675
r_scangle_it	5.708
r_dihedral_angle_1_deg	5.501
r_scbond_it	4.108
r_mcangle_it	2.431
r_angle_refined_deg	2.249
r_mcbond_it	1.712
r_nbtor_refined	0.317

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.976
r_dihedral_angle_4_deg	17.766
r_dihedral_angle_3_deg	14.675
r_scangle_it	5.708
r_dihedral_angle_1_deg	5.501
r_scbond_it	4.108
r_mcangle_it	2.431
r_angle_refined_deg	2.249
r_mcbond_it	1.712
r_nbtor_refined	0.317
r_nbd_refined	0.239
r_symmetry_hbond_refined	0.209
r_symmetry_vdw_refined	0.196
r_xyhbond_nbd_refined	0.186
r_chiral_restr	0.165
r_bond_refined_d	0.029
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10851
Nucleic Acid Atoms
Solvent Atoms	1777
Heterogen Atoms	72

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.