4MYQ | pdb_00004myq

Selective Inhibition of the Catalytic Domain Of Human Phosphodiesterase 4B With A-33

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3G45	PDB entry 3G45

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	VCID6271 PDE4 AT 7.9 MG/ML IN 20MM HEPES PH 7.5, 100 MM NACL, 1MM DTT, WITH 0.5MM A-33 AGAINST JCSG_ A10 (OPTIMIZATION SCREEN), 328.57MM POTASSIUM FORMATE, 24% W/V PEG 3350, CRYO 20% ETHYLENE GLYCOL AND 0.1MM COMPOUND, CRYSTAL TRACKING ID 232128E12, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K, temperature 289.0K

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.7	α = 90
b = 99.7	β = 90
c = 47.02	γ = 90

Symmetry
Space Group	P 42

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	RIGAKU SATURN 944+		2012-03-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

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	1.9	49.85	97.3	0.087	12.5	3.2	36759	35759	2	-3	18.71

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	1.9	1.95	86.7		0.483	2.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	PDB entry 3G45	1.9	49.85	2	36759	35759	1788	97.3	0.19	0.188	0.19	0.222	0.22	RANDOM	12.8

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]
0.12			0.12		-0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.805
r_dihedral_angle_4_deg	19.018
r_dihedral_angle_3_deg	13.778
r_dihedral_angle_1_deg	5.002
r_angle_refined_deg	1.487
r_angle_other_deg	1.013
r_chiral_restr	0.084
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_gen_planes_other	0.006
r_bond_other_d	0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2758
Nucleic Acid Atoms
Solvent Atoms	375
Heterogen Atoms	41

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling