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Crystal structure of the CTP-liganded (T-State) aspartate transcarbamoylase from the extremely thermophilic archaeon Sulfolobus acidocaldarius
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PG5 PDB Entry: 1PG5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 298 AMMONIUM SULFATE, SODIUM ACETATE
CTP soak, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.29 62.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.932 α = 90 b = 131.932 β = 90 c = 139.132 γ = 120
Symmetry Space Group P 63 2 2
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 2005-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8034 EMBL/DESY, HAMBURG X13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 50 98.2 24875 24875
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.56 96.6
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 (All) 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: 1PG5 2.6 20 20963 1123 98.09 0.22501 0.22501 0.22257 0.2239 0.27133 0.2264 RANDOM 46.349
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] 0.85 0.42 0.85 -1.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.288 r_dihedral_angle_4_deg 21.958 r_dihedral_angle_3_deg 19.495 r_dihedral_angle_1_deg 6.353 r_scangle_it 2.21 r_angle_refined_deg 1.44 r_scbond_it 1.417 r_mcangle_it 1.081 r_mcbond_it 0.619 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.288 r_dihedral_angle_4_deg 21.958 r_dihedral_angle_3_deg 19.495 r_dihedral_angle_1_deg 6.353 r_scangle_it 2.21 r_angle_refined_deg 1.44 r_scbond_it 1.417 r_mcangle_it 1.081 r_mcbond_it 0.619 r_nbtor_refined 0.312 r_symmetry_hbond_refined 0.256 r_nbd_refined 0.208 r_symmetry_vdw_refined 0.194 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3494 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing