3DYS

human phosphodiestrase-5'GMP complex (EP), produced by soaking with 20mM cGMP+20 mM MnCl2+20 mM MgCl2 for 2 hours, and flash-cooled to liquid nitrogen temperature when substrate was still abudant.


X-RAY DIFFRACTION

Crystallization

Crystal Properties
Matthews coefficientSolvent content
4.6973.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.992α = 90
b = 103.992β = 90
c = 269.762γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102006-06-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.0APS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.35099.40.07718.9466436242.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2.35059549671299.480.188460.185710.21224RANDOM33.706
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]
1.751.75-3.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.345
r_dihedral_angle_4_deg19.481
r_dihedral_angle_3_deg15.001
r_dihedral_angle_1_deg5.378
r_scangle_it2.473
r_scbond_it1.711
r_angle_refined_deg1.237
r_angle_other_deg0.92
r_mcangle_it0.917
r_mcbond_it0.843
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.345
r_dihedral_angle_4_deg19.481
r_dihedral_angle_3_deg15.001
r_dihedral_angle_1_deg5.378
r_scangle_it2.473
r_scbond_it1.711
r_angle_refined_deg1.237
r_angle_other_deg0.92
r_mcangle_it0.917
r_mcbond_it0.843
r_symmetry_vdw_other0.288
r_symmetry_vdw_refined0.254
r_nbd_refined0.218
r_nbd_other0.185
r_nbtor_refined0.18
r_xyhbond_nbd_refined0.169
r_mcbond_other0.132
r_symmetry_hbond_refined0.119
r_nbtor_other0.087
r_chiral_restr0.072
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
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 AtomsNumber
Protein Atoms5384
Nucleic Acid Atoms
Solvent Atoms463
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement