1WOJ | pdb_00001woj

Crystal structure of human phosphodiesterase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	PEG300, sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.91	33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.386	α = 90
b = 55.348	β = 90
c = 78.757	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	CCD	ADSC QUANTUM 210		2003-05-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.00	Photon Factory	AR-NW12A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.8	40	98.2	0.057	9.4	6.5		18263

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.8	1.9	92		0.191	3.8	4.9

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 (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SIR	THROUGHOUT	1.8	40	17284	934	97.98	0.19406	0.19238	0.22529	RANDOM	21.465

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]
0.11			0.89		-1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.366
r_scangle_it	3.732
r_scbond_it	2.153
r_mcangle_it	1.379
r_angle_refined_deg	1.083
r_angle_other_deg	0.721
r_mcbond_it	0.709
r_symmetry_vdw_other	0.26
r_nbd_other	0.234
r_nbd_refined	0.205
r_xyhbond_nbd_refined	0.149
r_symmetry_vdw_refined	0.107
r_symmetry_hbond_refined	0.096
r_nbtor_other	0.079
r_chiral_restr	0.063
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1646
Nucleic Acid Atoms
Solvent Atoms	96
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
SHARP	phasing