1XMY | pdb_00001xmy

Catalytic Domain Of Human Phosphodiesterase 4B In Complex With (R)-Rolipram

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	10	277	ammonium sulfate and lithium sulfate, pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.67	α = 90
b = 94.633	β = 90
c = 106.432	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		2004-07-20	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	2.4	70.71	99.15	0.096	4.7	4.1	34006	34006

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.462	99.2		0.759	3.7	2591

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	2.4	70.71	34006	34006	1792	99.15	0.2454	0.24264	0.2434	0.29805	0.2949	RANDOM	22.28

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]
-3.59			-1.87		5.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	3.999
r_scangle_it	3.714
r_scbond_it	2.491
r_angle_refined_deg	2.04
r_mcangle_it	1.448
r_angle_other_deg	1.055
r_mcbond_it	0.832
r_symmetry_vdw_refined	0.411
r_symmetry_vdw_other	0.256
r_symmetry_hbond_refined	0.235
r_nbd_refined	0.233
r_nbd_other	0.233
r_xyhbond_nbd_refined	0.176
r_metal_ion_refined	0.162
r_chiral_restr	0.119
r_nbtor_other	0.096
r_bond_refined_d	0.025
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	61
Heterogen Atoms	44

Software

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