4USV

Crystal structure of human soluble Adenylyl Cyclase with pyrophosphate resulting from soaking with ATP and Calcium


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
160.1 M SODIUM ACETATE PH 4.8, 0.2 M TRI-SODIUM-CITRATE, 15% (W/V) PEG 4000, 10% (V/V) GLYCEROL
Crystal Properties
Matthews coefficientSolvent content
2.454

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.87α = 90
b = 100.87β = 90
c = 97.15γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MCOLLIMATOR2013-07-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.1BESSY14.1

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
1287.361000.0718.116.3379192
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)
122.051000.82.26.5

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 REPLACEMENTTHROUGHOUTPDB ENTRY 4CLK287.3635990192999.950.162350.159940.20893RANDOM43.485
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]
0.470.240.47-1.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.441
r_dihedral_angle_4_deg15.916
r_dihedral_angle_3_deg15.232
r_dihedral_angle_1_deg6.323
r_scbond_it4.495
r_mcangle_it4.433
r_mcbond_it3.213
r_mcbond_other3.047
r_angle_refined_deg1.993
r_angle_other_deg0.941
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.441
r_dihedral_angle_4_deg15.916
r_dihedral_angle_3_deg15.232
r_dihedral_angle_1_deg6.323
r_scbond_it4.495
r_mcangle_it4.433
r_mcbond_it3.213
r_mcbond_other3.047
r_angle_refined_deg1.993
r_angle_other_deg0.941
r_chiral_restr0.127
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.001
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3607
Nucleic Acid Atoms
Solvent Atoms185
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing