3O0J | pdb_00003o0j

PDE4B In complex with ligand an2898

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	hanging drop vapor diffusion	7.4	298	MgCl2, pH 7.4, hanging drop vapor diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.611	α = 90
b = 53.611	β = 90
c = 229.014	γ = 90

Symmetry
Space Group	P 43 21 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	PILATUS				M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.918	SLS	X06SA

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	1.95	57.26	98.3	0.058		11.6	25477	25081

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	1.95	2.03	85.1		0.383		4.7	2396

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	OTHER	THROUGHOUT	1.95	57.26	23826	1254	98.48	0.1867	0.1841	0.19	0.2365	0.24	RANDOM	35.2541

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]
1.63			1.63		-3.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.613
r_dihedral_angle_4_deg	14.151
r_dihedral_angle_3_deg	12.777
r_scangle_it	5.691
r_dihedral_angle_1_deg	4.949
r_scbond_it	4.383
r_mcangle_it	2.715
r_mcbond_it	2.234
r_angle_refined_deg	1.065
r_angle_other_deg	0.751
r_mcbond_other	0.554
r_symmetry_vdw_other	0.243
r_nbd_refined	0.216
r_nbtor_refined	0.182
r_nbd_other	0.16
r_xyhbond_nbd_refined	0.155
r_symmetry_hbond_refined	0.149
r_symmetry_vdw_refined	0.1
r_nbtor_other	0.081
r_metal_ion_refined	0.078
r_chiral_restr	0.065
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2615
Nucleic Acid Atoms
Solvent Atoms	134
Heterogen Atoms	79

Software

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