4CLS

Crystal structure of human soluble Adenylyl Cyclase with Pyrophosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4CLFPDB ENTRY 4CLF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62770.1 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
2.7555

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.09α = 90
b = 100.09β = 90
c = 97.75γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MCOLLIMATOR2013-10-23MSINGLE 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
11.8586.681000.1049447385-3
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)
11.851.91000.8871.64.1

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 4CLF1.8586.6845014237199.810.175580.17360.2138RANDOM35.669
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]
0.130.070.13-0.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.568
r_dihedral_angle_3_deg15.599
r_dihedral_angle_4_deg14.75
r_long_range_B_refined8.074
r_long_range_B_other8.073
r_dihedral_angle_1_deg6.345
r_scangle_other5.684
r_mcangle_other4.079
r_mcangle_it4.078
r_scbond_it3.779
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.568
r_dihedral_angle_3_deg15.599
r_dihedral_angle_4_deg14.75
r_long_range_B_refined8.074
r_long_range_B_other8.073
r_dihedral_angle_1_deg6.345
r_scangle_other5.684
r_mcangle_other4.079
r_mcangle_it4.078
r_scbond_it3.779
r_scbond_other3.768
r_mcbond_it2.669
r_mcbond_other2.667
r_angle_refined_deg1.923
r_angle_other_deg0.924
r_chiral_restr0.122
r_bond_refined_d0.019
r_gen_planes_refined0.009
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3638
Nucleic Acid Atoms
Solvent Atoms162
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing