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Atomic resolution structure of SAICAR-synthase from Saccharomyces cerevisiae complexed with ADP, AICAR, succinate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1A48 PDB ENTRY 1A48
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 AMMONIUM SUPHATE, ATP, AICAR, MG, ASP, pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.1 40.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.683 α = 90 b = 61.851 β = 90 c = 76.893 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH MIRRORS 1997-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1 18 96.4 0.05 27 4 150732 7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1 1.03 93.6 0.25 3 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1A48 1 17 146100 4546 96.8 0.116 0.115 0.1267 0.13 0.1423 RANDOM 8.58
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.052 r_dihedral_angle_4_deg 21.248 r_dihedral_angle_3_deg 12.275 r_dihedral_angle_1_deg 6.527 r_scangle_it 3.077 r_scbond_it 2.43 r_angle_refined_deg 1.98 r_mcangle_it 1.872 r_angle_other_deg 1.717 r_mcbond_it 1.501
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.052 r_dihedral_angle_4_deg 21.248 r_dihedral_angle_3_deg 12.275 r_dihedral_angle_1_deg 6.527 r_scangle_it 3.077 r_scbond_it 2.43 r_angle_refined_deg 1.98 r_mcangle_it 1.872 r_angle_other_deg 1.717 r_mcbond_it 1.501 r_nbd_refined 0.253 r_symmetry_vdw_other 0.25 r_symmetry_vdw_refined 0.229 r_symmetry_hbond_refined 0.227 r_nbtor_refined 0.211 r_nbd_other 0.204 r_xyhbond_nbd_refined 0.184 r_chiral_restr 0.158 r_nbtor_other 0.097 r_bond_refined_d 0.023 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.002 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 Atoms Number Protein Atoms 2406 Nucleic Acid Atoms Solvent Atoms 733 Heterogen Atoms 158
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing