4UST

Crystal structure of human soluble Adenylyl Cyclase with pyrophosphate resulting from soaking with GTP and Magnesium


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 = 100.34α = 90
b = 100.34β = 90
c = 97.42γ = 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
11.986.999.90.0711.354438262
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)
11.91.9599.90.621.923.8

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 4CLK1.986.941625220199.80.1630.160910.20248RANDOM38.645
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]
0.280.140.28-0.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.162
r_dihedral_angle_3_deg15.661
r_dihedral_angle_4_deg12.577
r_dihedral_angle_1_deg6.236
r_scbond_it4.352
r_mcangle_it4.26
r_mcbond_it2.952
r_mcbond_other2.947
r_angle_refined_deg1.941
r_angle_other_deg0.924
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.162
r_dihedral_angle_3_deg15.661
r_dihedral_angle_4_deg12.577
r_dihedral_angle_1_deg6.236
r_scbond_it4.352
r_mcangle_it4.26
r_mcbond_it2.952
r_mcbond_other2.947
r_angle_refined_deg1.941
r_angle_other_deg0.924
r_chiral_restr0.126
r_bond_refined_d0.02
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 Atoms3620
Nucleic Acid Atoms
Solvent Atoms221
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing