2CNU

Atomic resolution structure of SAICAR-synthase from Saccharomyces cerevisiae complexed with aspartic acid


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5TRIS-HCL BUFFER, PH 7.5, ASPARTIC ACID, AMMONIUM SULPHATE
Crystal Properties
Matthews coefficientSolvent content
2.140.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.023α = 90
b = 62.497β = 90
c = 78.273γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMIRRORS1997-02-20MSINGLE 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
11.052494.40.0524413199212
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)
11.051.0894.40.3334

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 1A481.0523.9712530666441000.1340.1320.159RANDOM13.06
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]
-0.5-0.390.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg19.971
r_dihedral_angle_4_deg19.971
r_dihedral_angle_1_deg6.686
r_scangle_it4.956
r_scbond_it4.044
r_mcangle_it2.988
r_mcbond_it2.48
r_angle_refined_deg2.242
r_angle_other_deg2.056
r_nbd_refined0.352
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg19.971
r_dihedral_angle_4_deg19.971
r_dihedral_angle_1_deg6.686
r_scangle_it4.956
r_scbond_it4.044
r_mcangle_it2.988
r_mcbond_it2.48
r_angle_refined_deg2.242
r_angle_other_deg2.056
r_nbd_refined0.352
r_nbd_other0.352
r_nbtor_refined0.223
r_symmetry_hbond_refined0.216
r_symmetry_vdw_other0.199
r_symmetry_vdw_refined0.188
r_chiral_restr0.147
r_xyhbond_nbd_refined0.103
r_bond_refined_d0.023
r_gen_planes_refined0.012
r_gen_planes_other0.004
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_nbtor_other
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 Atoms2403
Nucleic Acid Atoms
Solvent Atoms708
Heterogen Atoms62

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing