5X73

The crystal Structure PDE delta in complex with R-p9


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP52778% v/v Tacsimate, 20% w/v Polyethylene glycol 3350
Crystal Properties
Matthews coefficientSolvent content
2.9858.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.55α = 90
b = 55.55β = 90
c = 115.34γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100AREA DETECTORADSC QUANTUM 315r2016-01-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.97941SSRFBL17U

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
12.55099.40.0720.02823.758.27571
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.5499.70.350.137.818.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4JV62.548.11708139898.560.198290.195460.24528RANDOM65.725
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]
-0.05-0.02-0.050.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg45.183
r_dihedral_angle_4_deg28.429
r_dihedral_angle_3_deg14.129
r_long_range_B_other11.885
r_long_range_B_refined11.869
r_scangle_other9.44
r_dihedral_angle_1_deg7.626
r_mcangle_it6.667
r_mcangle_other6.665
r_scbond_it6.627
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg45.183
r_dihedral_angle_4_deg28.429
r_dihedral_angle_3_deg14.129
r_long_range_B_other11.885
r_long_range_B_refined11.869
r_scangle_other9.44
r_dihedral_angle_1_deg7.626
r_mcangle_it6.667
r_mcangle_other6.665
r_scbond_it6.627
r_scbond_other6.623
r_mcbond_it5.225
r_mcbond_other5.218
r_angle_refined_deg1.715
r_angle_other_deg0.866
r_chiral_restr0.092
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1209
Nucleic Acid Atoms
Solvent Atoms23
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling