7UYQ

Structure of GTP binds to Cyclic GMP AMP synthase (cGAS) through Mg coordination


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5277.150.2 M ammonium acetate, 32% MPD, with 0.1 M Bis-Tris pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.5651.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.745α = 90
b = 99.578β = 90
c = 142.001γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-10-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS-II BEAMLINE 17-ID-20.9793NSLS-II17-ID-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.5728.9299.40.090.0980.0380.99812.86.735696
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.572.6895.90.810.8780.3350.766.6

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 REPLACEMENTTHROUGHOUT4LEZ2.5728.9233857171699.370.19790.19570.2415RANDOM65.737
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]
1.09-1.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.192
r_dihedral_angle_4_deg15.638
r_dihedral_angle_3_deg15.137
r_dihedral_angle_1_deg6.277
r_angle_refined_deg1.325
r_angle_other_deg1.105
r_chiral_restr0.071
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.192
r_dihedral_angle_4_deg15.638
r_dihedral_angle_3_deg15.137
r_dihedral_angle_1_deg6.277
r_angle_refined_deg1.325
r_angle_other_deg1.105
r_chiral_restr0.071
r_bond_refined_d0.011
r_gen_planes_refined0.006
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5687
Nucleic Acid Atoms1464
Solvent Atoms47
Heterogen Atoms132

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
REFMACrefinement
PDB_EXTRACTdata extraction