3DYL

human phosphdiesterase 9 substrate complex (ES complex)


X-RAY DIFFRACTION

Crystallization

Crystal Properties
Matthews coefficientSolvent content
4.6773.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.787α = 90
b = 103.787β = 90
c = 269.799γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102007-06-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ DW1.5418APS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.796.6737247372472
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.81000.77127.34075

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 SYNTHESISTHROUGHOUT2.796.6737247421699.720.190890.187570.21902RANDOM42.135
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]
2.062.06-4.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.576
r_dihedral_angle_4_deg21.117
r_dihedral_angle_3_deg17.289
r_dihedral_angle_1_deg6.055
r_scangle_it3.421
r_scbond_it2.318
r_angle_refined_deg1.931
r_mcangle_it1.262
r_angle_other_deg1.118
r_mcbond_it1.086
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.576
r_dihedral_angle_4_deg21.117
r_dihedral_angle_3_deg17.289
r_dihedral_angle_1_deg6.055
r_scangle_it3.421
r_scbond_it2.318
r_angle_refined_deg1.931
r_mcangle_it1.262
r_angle_other_deg1.118
r_mcbond_it1.086
r_symmetry_vdw_other0.292
r_nbd_refined0.253
r_symmetry_vdw_refined0.25
r_nbtor_refined0.202
r_nbd_other0.2
r_mcbond_other0.186
r_xyhbond_nbd_refined0.169
r_metal_ion_refined0.169
r_symmetry_hbond_refined0.15
r_chiral_restr0.106
r_nbtor_other0.096
r_bond_refined_d0.023
r_gen_planes_refined0.007
r_gen_planes_other0.003
r_bond_other_d0.002
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 AtomsNumber
Protein Atoms5412
Nucleic Acid Atoms
Solvent Atoms177
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement