3G4I

Crystal structure of human phosphodiesterase 4d with d155871

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	100MM HEPES PH 7.5, 35% ETHYLENE GLYCOL, 5% GLYCEROL, 22% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.865	α = 90
b = 113.241	β = 90
c = 161.22	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	100					M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.97	ALS	5.0.1

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	1.9	50	92.9	0.057	8.9	3.8		132652

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)
	1.9	1.97	93.3		0.581		2.9

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.9	50	132466	6596		0.183	0.181	0.215	RANDOM	20.39

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]
0.73			-0.86		0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.127
r_dihedral_angle_4_deg	16.616
r_dihedral_angle_3_deg	13.623
r_dihedral_angle_1_deg	4.984
r_scangle_it	2.609
r_scbond_it	1.786
r_angle_refined_deg	1.157
r_mcangle_it	1.093
r_angle_other_deg	0.945
r_mcbond_it	0.789
r_symmetry_vdw_other	0.253
r_symmetry_vdw_refined	0.231
r_nbd_refined	0.215
r_xyhbond_nbd_refined	0.195
r_symmetry_hbond_refined	0.188
r_nbd_other	0.183
r_nbtor_refined	0.17
r_mcbond_other	0.155
r_nbtor_other	0.083
r_chiral_restr	0.066
r_metal_ion_refined	0.015
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10655
Nucleic Acid Atoms
Solvent Atoms	1203
Heterogen Atoms	159

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling