2CNQ

Atomic resolution structure of SAICAR-synthase from Saccharomyces cerevisiae complexed with ADP, AICAR, succinate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1A48PDB ENTRY 1A48

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5AMMONIUM SUPHATE, ATP, AICAR, MG, ASP, pH 7.50
Crystal Properties
Matthews coefficientSolvent content
2.140.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.683α = 90
b = 61.851β = 90
c = 76.893γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS1997-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X11EMBL/DESY, HAMBURGX11

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
111896.40.052741507327
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)
111.0393.60.2534

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 1A48117146100454696.80.1160.1150.13RANDOM8.58
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]
0.32-0.15-0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.052
r_dihedral_angle_4_deg21.248
r_dihedral_angle_3_deg12.275
r_dihedral_angle_1_deg6.527
r_scangle_it3.077
r_scbond_it2.43
r_angle_refined_deg1.98
r_mcangle_it1.872
r_angle_other_deg1.717
r_mcbond_it1.501
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.052
r_dihedral_angle_4_deg21.248
r_dihedral_angle_3_deg12.275
r_dihedral_angle_1_deg6.527
r_scangle_it3.077
r_scbond_it2.43
r_angle_refined_deg1.98
r_mcangle_it1.872
r_angle_other_deg1.717
r_mcbond_it1.501
r_nbd_refined0.253
r_symmetry_vdw_other0.25
r_symmetry_vdw_refined0.229
r_symmetry_hbond_refined0.227
r_nbtor_refined0.211
r_nbd_other0.204
r_xyhbond_nbd_refined0.184
r_chiral_restr0.158
r_nbtor_other0.097
r_bond_refined_d0.023
r_gen_planes_refined0.01
r_gen_planes_other0.003
r_bond_other_d0.002
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
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 Atoms2406
Nucleic Acid Atoms
Solvent Atoms733
Heterogen Atoms158

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing