☰ Navigation Tabs
Crystal Structure of Aquifex Dihydroorotase Activated by Aspartate Transcarbamoylase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ML4 1xrtA, 1ml4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 3 mg/mL protein in 10mM Hepes, 10 mM sodium citrate, 2 mM DTT mixed 6:1 with 25% ethylene glycol, 10mM BaCL2 and equilibrated with same., pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.52 65.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.439 α = 90 b = 158.439 β = 90 c = 233.553 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD ADSC QUANTUM 270 2006-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.00000 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.3 65 99.97 0.8 23.83 5.8 47628 47614 34.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 99.4 0.546 2.96 5.7 9768
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 SAD THROUGHOUT 1xrtA, 1ml4 2.3 65 47628 47614 2544 99.97 0.1665 0.16646 0.16444 0.1632 0.20404 0.2018 RANDOM 34.423
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] 0.11 0.06 0.11 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.416 r_dihedral_angle_4_deg 21.933 r_dihedral_angle_3_deg 16.876 r_dihedral_angle_1_deg 8.984 r_scangle_it 4.502 r_scbond_it 2.926 r_angle_refined_deg 1.815 r_mcangle_it 1.665 r_mcbond_it 1.069 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.416 r_dihedral_angle_4_deg 21.933 r_dihedral_angle_3_deg 16.876 r_dihedral_angle_1_deg 8.984 r_scangle_it 4.502 r_scbond_it 2.926 r_angle_refined_deg 1.815 r_mcangle_it 1.665 r_mcbond_it 1.069 r_nbtor_refined 0.309 r_symmetry_hbond_refined 0.272 r_nbd_refined 0.213 r_symmetry_vdw_refined 0.205 r_xyhbond_nbd_refined 0.204 r_chiral_restr 0.132 r_bond_refined_d 0.02 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5632 Nucleic Acid Atoms Solvent Atoms 422 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing