5IV3

Crystal structure of human soluble adenylyl cyclase in complex with alpha,beta-methyleneadenosine-5'-triphosphate and the allosteric inhibitor LRE1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4CLK 

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
2.3247

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.032α = 90
b = 100.032β = 90
c = 98.658γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-09-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.918409BESSY14.1

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
11.8644.6199.90.12210.24.646795
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)
11.861.9899.71.2811.34.4

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 REPLACEMENTTHROUGHOUT4clk1.8644.6144694210199.880.178060.175940.22308RANDOM34.4
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]
0.330.160.33-1.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.33
r_dihedral_angle_4_deg17.581
r_dihedral_angle_3_deg14.928
r_long_range_B_refined8.75
r_long_range_B_other8.748
r_dihedral_angle_1_deg6.833
r_scangle_other6.394
r_mcangle_it4.797
r_mcangle_other4.796
r_scbond_it4.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.33
r_dihedral_angle_4_deg17.581
r_dihedral_angle_3_deg14.928
r_long_range_B_refined8.75
r_long_range_B_other8.748
r_dihedral_angle_1_deg6.833
r_scangle_other6.394
r_mcangle_it4.797
r_mcangle_other4.796
r_scbond_it4.29
r_scbond_other4.28
r_mcbond_it3.296
r_mcbond_other3.295
r_angle_refined_deg2.035
r_angle_other_deg1.063
r_chiral_restr0.128
r_bond_refined_d0.019
r_gen_planes_refined0.01
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 Atoms3608
Nucleic Acid Atoms
Solvent Atoms267
Heterogen Atoms88

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing