5X72

The crystal Structure PDE delta in complex with (rac)-p9


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2770.2 M Ammonium citrate dibasic, 20% w/v Polyethylene glycol 3350
Crystal Properties
Matthews coefficientSolvent content
2.9558.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.568α = 90
b = 55.568β = 90
c = 115.465γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100AREA DETECTORADSC QUANTUM 315r2015-12-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.97915SSRFBL17U

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
11.955099.70.0660.01938.6113.915663
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)
11.951.981000.4810.1327.414.2

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 REPLACEMENTTHROUGHOUT4JV61.9548.121452474297.370.189680.187480.23142RANDOM27.645
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]
-0.12-0.06-0.120.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.947
r_dihedral_angle_4_deg14.844
r_dihedral_angle_3_deg13.523
r_dihedral_angle_1_deg7.572
r_long_range_B_refined6.072
r_long_range_B_other6.07
r_scangle_other3.481
r_scbond_it2.184
r_scbond_other2.182
r_mcangle_it2.168
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.947
r_dihedral_angle_4_deg14.844
r_dihedral_angle_3_deg13.523
r_dihedral_angle_1_deg7.572
r_long_range_B_refined6.072
r_long_range_B_other6.07
r_scangle_other3.481
r_scbond_it2.184
r_scbond_other2.182
r_mcangle_it2.168
r_mcangle_other2.166
r_angle_refined_deg2.089
r_mcbond_other1.373
r_mcbond_it1.372
r_angle_other_deg0.971
r_chiral_restr0.131
r_bond_refined_d0.023
r_gen_planes_refined0.013
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms1212
Nucleic Acid Atoms
Solvent Atoms86
Heterogen Atoms48

Software

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