4JIB | pdb_00004jib

Crystal structure of of PDE2-inhibitor complex

X-RAY DIFFRACTION

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Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.88	α = 109.67
b = 74.132	β = 88.72
c = 91.802	γ = 88.97

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 17-ID	1.00	APS	17-ID

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	1.72	86.39	96.2	0.066	11.7	3.9		142966

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	1.72	1.78	85.9		0.452		3.6	12773

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	FOURIER SYNTHESIS	THROUGHOUT	1.72	50	142327	7141	96.6	0.1905	0.188	0.187	0.2402	0.2369	RANDOM	23.7846

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]
-1.04	0.54	0.9	0.59	0.01	0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.403
r_dihedral_angle_4_deg	16.085
r_dihedral_angle_3_deg	13.992
r_dihedral_angle_1_deg	5.026
r_scangle_it	3.614
r_scbond_it	2.496
r_angle_refined_deg	1.49
r_mcangle_it	1.458
r_mcbond_it	0.942
r_nbtor_refined	0.308
r_nbd_refined	0.209
r_symmetry_vdw_refined	0.173
r_symmetry_hbond_refined	0.133
r_xyhbond_nbd_refined	0.125
r_chiral_restr	0.093
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10935
Nucleic Acid Atoms
Solvent Atoms	1435
Heterogen Atoms	132

Software

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