5IV4

Crystal structure of the human soluble adenylyl cyclase in complex with the allosteric inhibitor LRE1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5277.15100 mM sodium acetate pH 4.8 200 mM tri-sodium-citrate 15% (w/v) PEG 4000 10% (v/v) glycerol
Crystal Properties
Matthews coefficientSolvent content
2.347

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.298α = 90
b = 99.298β = 90
c = 99.386γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-02-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.918007BESSY14.1

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
11.7944.4299.90.11516.311.4599809
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)
11.791.999.51.1922.0711.2

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 DIFFRACTIONTHROUGHOUT1.7944.4249787262199.920.1620.159720.20626RANDOM30.704
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]
0.270.130.27-0.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.729
r_dihedral_angle_4_deg18.356
r_dihedral_angle_3_deg14.49
r_long_range_B_refined8.822
r_long_range_B_other8.821
r_scangle_other6.644
r_dihedral_angle_1_deg6.436
r_scbond_it4.451
r_scbond_other4.437
r_mcangle_it4.339
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.729
r_dihedral_angle_4_deg18.356
r_dihedral_angle_3_deg14.49
r_long_range_B_refined8.822
r_long_range_B_other8.821
r_scangle_other6.644
r_dihedral_angle_1_deg6.436
r_scbond_it4.451
r_scbond_other4.437
r_mcangle_it4.339
r_mcangle_other4.339
r_mcbond_it3.241
r_mcbond_other3.212
r_angle_refined_deg2.079
r_angle_other_deg1.133
r_chiral_restr0.159
r_bond_refined_d0.021
r_gen_planes_refined0.011
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 Atoms3660
Nucleic Acid Atoms
Solvent Atoms358
Heterogen Atoms76

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Cootmodel building
MOLREPphasing
XSCALEdata scaling