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Atomic resolution structure of SAICAR-synthase from Saccharomyces cerevisiae complexed with aspartic acid
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 TRIS-HCL BUFFER, PH 7.5, ASPARTIC ACID, AMMONIUM SULPHATE
Crystal Properties Matthews coefficient Solvent content 2.1 40.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.023 α = 90 b = 62.497 β = 90 c = 78.273 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 IMAGE PLATE MARRESEARCH MIRRORS 1997-02-20 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 1.05 24 94.4 0.05 24 4 131992 12
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 1.05 1.08 94.4 0.33 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 1.05 23.97 125306 6644 100 0.134 0.132 0.1501 0.159 0.1728 RANDOM 13.06
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 -0.39 0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.971 r_dihedral_angle_4_deg 19.971 r_dihedral_angle_1_deg 6.686 r_scangle_it 4.956 r_scbond_it 4.044 r_mcangle_it 2.988 r_mcbond_it 2.48 r_angle_refined_deg 2.242 r_angle_other_deg 2.056 r_nbd_refined 0.352
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.971 r_dihedral_angle_4_deg 19.971 r_dihedral_angle_1_deg 6.686 r_scangle_it 4.956 r_scbond_it 4.044 r_mcangle_it 2.988 r_mcbond_it 2.48 r_angle_refined_deg 2.242 r_angle_other_deg 2.056 r_nbd_refined 0.352 r_nbd_other 0.352 r_nbtor_refined 0.223 r_symmetry_hbond_refined 0.216 r_symmetry_vdw_other 0.199 r_symmetry_vdw_refined 0.188 r_chiral_restr 0.147 r_xyhbond_nbd_refined 0.103 r_bond_refined_d 0.023 r_gen_planes_refined 0.012 r_gen_planes_other 0.004 r_bond_other_d 0.002 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 Atoms Number Protein Atoms 2403 Nucleic Acid Atoms Solvent Atoms 708 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing