1TB5 | pdb_00001tb5

Catalytic Domain Of Human Phosphodiesterase 4B In Complex With AMP

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	10	277	ammonium sulfate, lithium sulfate, pH 10, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.547	α = 90
b = 94.241	β = 90
c = 107.243	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	CCD	ADSC QUANTUM 210		2003-08-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.1	ALS	8.3.1

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	2.15	70.71		0.079	9.2	4.7	46988	46988

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	2.15	2.206	100		0.751	1.63	4.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	2.15	70.71	46988	46988	2505	98.91	0.23544	0.23362	0.24	0.26822	0.27	RANDOM	29.352

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]
-3.6			0.84		2.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	3.214
r_scangle_it	3.092
r_scbond_it	1.974
r_angle_refined_deg	1.502
r_mcangle_it	1.113
r_angle_other_deg	0.937
r_mcbond_it	0.606
r_symmetry_vdw_other	0.313
r_nbd_other	0.222
r_nbd_refined	0.221
r_xyhbond_nbd_refined	0.178
r_symmetry_hbond_refined	0.177
r_symmetry_vdw_refined	0.143
r_metal_ion_refined	0.121
r_chiral_restr	0.096
r_nbtor_other	0.093
r_bond_refined_d	0.015
r_gen_planes_refined	0.009
r_gen_planes_other	0.008
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5226
Nucleic Acid Atoms
Solvent Atoms	69
Heterogen Atoms	50

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
ELVES	data scaling
EPMR	phasing