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Crystal Structure of the Aquifex aeolicus primase (Zinc Binding and RNA Polymerase Domains)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Low-resolution Aquifex aeolicus DnaG from Tm-soak MAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7.5 291 18-22% EtOH, 55 mM HEPES, 100 mM NaCl, pH 7.5, Microbatch, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.13 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.222 α = 90 b = 66.403 β = 90 c = 138.157 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 ADSC QUANTUM 210 2003-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 0.9792 ALS 8.3.1
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 40 99 0.078 14.3 3.45 27417 25989 2 2
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 2.07 93.8 0.286 3.3 3.2 2547
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 MOLECULAR REPLACEMENT THROUGHOUT Low-resolution Aquifex aeolicus DnaG from Tm-soak MAD 2 40 25989 25989 1377 98.93 0.20488 0.20488 0.20304 0.2014 0.23826 0.2343 RANDOM 26.19
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] -1.63 1.9 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.75 r_scangle_it 4.957 r_scbond_it 2.886 r_mcangle_it 2.055 r_angle_refined_deg 1.223 r_mcbond_it 1.155 r_nbd_refined 0.214 r_symmetry_vdw_refined 0.197 r_symmetry_hbond_refined 0.173 r_xyhbond_nbd_refined 0.149
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.75 r_scangle_it 4.957 r_scbond_it 2.886 r_mcangle_it 2.055 r_angle_refined_deg 1.223 r_mcbond_it 1.155 r_nbd_refined 0.214 r_symmetry_vdw_refined 0.197 r_symmetry_hbond_refined 0.173 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.103 r_metal_ion_refined 0.068 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3260 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing