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Crystal Structure of the Aquifex Reactor Complex Formed by Dihydroorotase (H180A, H232A) with Dihydroorotate and Aspartate Transcarbamoylase with N-(phosphonacetyl)-L-aspartate (PALA)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D6N PDB ENTRY 3D6N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 THE CRYSTALS WERE GROWN AT ROOM TEMPERATURE IN HANGING-DROPS. THE HETERO DODECAMER WAS BUFFER EXCHANGED INTO 10 MM HEPES, 1 MM TCEP PH 7.5, AT A FINAL PROTEIN CONCENTRATION OF 3.0 MG/ML. DHO-ATC SOLUTION (3-6 UL) WAS MIXED WITH 1 UL OF RESERVOIR SOLUTION (30% ETHYLENE GLYCOL) FOLLOWED BY 10% OF THE DROP VOLUME (V/V) OF 100 MM BARIUM CHLORIDE. THE FINAL CRYSTALLIZATION PH WAS 6.3.
Crystal Properties Matthews coefficient Solvent content 3.17 61.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.152 α = 90 b = 157.152 β = 90 c = 233.244 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 100 CCD MARRESEARCH MAR300 BE LENSES 2009-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G APS 21-ID-G
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 2.2 77.85 99.9 0.1 16.2 8.8 53365 41.7
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 2.2 2.32 100 0.76 2.3 8.8
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 3D6N 2.2 77.85 53365 2846 99.94 0.16282 0.16066 0.1572 0.20304 0.1974 RANDOM 41.256
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] -0.27 -0.14 -0.27 0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.837 r_dihedral_angle_4_deg 23.094 r_dihedral_angle_3_deg 15.736 r_dihedral_angle_1_deg 6.491 r_scangle_it 4.184 r_scbond_it 2.588 r_angle_refined_deg 1.558 r_mcangle_it 1.423 r_mcbond_it 0.738 r_chiral_restr 0.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.837 r_dihedral_angle_4_deg 23.094 r_dihedral_angle_3_deg 15.736 r_dihedral_angle_1_deg 6.491 r_scangle_it 4.184 r_scbond_it 2.588 r_angle_refined_deg 1.558 r_mcangle_it 1.423 r_mcbond_it 0.738 r_chiral_restr 0.104 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 5622 Nucleic Acid Atoms Solvent Atoms 445 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALEPACK data scaling ARP/wARP phasing