3ITM | pdb_00003itm

Catalytic domain of hPDE2A

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	Reservoir - 20% PDEG 3350, 0.2M tri-sodium citrate. Protein - 25mM Hepes pH7.5, 25mM NaCl, 2mM TCEP, 10ug/mL E-64, 1ug/mL pepstatin., VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.017	α = 90
b = 108.017	β = 90
c = 515.563	γ = 120

Symmetry
Space Group	P 61 2 2

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 210			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.00	APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.49	50	84.3	0.089	19.36	6.52	64064	54006		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.49	2.58	38.1		0.318	2.19	3.1

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.49	50	51187	2756	84.55	0.22982	0.22686	0.22	0.28648	0.27	RANDOM	43.289

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]
0.71	0.35		0.71		-1.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.052
r_dihedral_angle_3_deg	21.245
r_dihedral_angle_4_deg	19.153
r_dihedral_angle_1_deg	5.74
r_scangle_it	3.13
r_scbond_it	2.144
r_angle_refined_deg	2.029
r_mcangle_it	1.058
r_mcbond_it	0.689
r_nbtor_refined	0.323

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.052
r_dihedral_angle_3_deg	21.245
r_dihedral_angle_4_deg	19.153
r_dihedral_angle_1_deg	5.74
r_scangle_it	3.13
r_scbond_it	2.144
r_angle_refined_deg	2.029
r_mcangle_it	1.058
r_mcbond_it	0.689
r_nbtor_refined	0.323
r_symmetry_vdw_refined	0.274
r_nbd_refined	0.246
r_symmetry_hbond_refined	0.192
r_xyhbond_nbd_refined	0.172
r_chiral_restr	0.14
r_metal_ion_refined	0.094
r_bond_refined_d	0.033
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10280
Nucleic Acid Atoms
Solvent Atoms	163
Heterogen Atoms	4

Software

Software
Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.