2WEY | pdb_00002wey

Human PDE-papaverine complex obtained by ligand soaking of cross- linked protein crystals

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OUP	PDB ENTRY 2OUP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.25		16% PEG3350, 60 MM BETA-MERCAPTOETHANOL,0.1 M HEPES PH 7.25,0.2 M MGCL2

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.84	α = 90
b = 81.57	β = 90
c = 157.55	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	IMAGE PLATE	RIGAKU IMAGE PLATE	VARIMAX MIRRORS	2008-08-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300

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	2.8	56.7	100	0.136	13.3	6.5		15959		6	72.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.95	99.9		0.69	0.694	2.2	5.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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 2OUP	2.8	56.7	15959	843	100	0.242	0.239	0.23	0.3	0.29	RANDOM	67.06

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]
9.84			-6.33		-3.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.272
r_dihedral_angle_3_deg	16.765
r_dihedral_angle_4_deg	16.012
r_dihedral_angle_1_deg	4.748
r_angle_refined_deg	1.049
r_scangle_it	1.032
r_mcangle_it	0.86
r_scbond_it	0.633
r_mcbond_it	0.471
r_nbtor_refined	0.299
r_nbd_refined	0.207
r_symmetry_vdw_refined	0.195
r_xyhbond_nbd_refined	0.138
r_symmetry_hbond_refined	0.114
r_metal_ion_refined	0.096
r_chiral_restr	0.07
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
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	5258
Nucleic Acid Atoms
Solvent Atoms	23
Heterogen Atoms	54

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALEPACK	data scaling
MOLREP	phasing