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Structure of AMPPCP-bound DnaA from Aquifex aeolicus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L8Q PDB ENTRY 1L8Q RESIDUES 77 TO 240
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 292 50mM Na cacodylate, 125mM KCl, 125mM Kbr, 5% Glycerol, 25% 1,2-Propanediol, 5% PEG MME2K, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K, pH 6.50
Crystal Properties Matthews coefficient Solvent content 3.88 68.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.076 α = 90 b = 117.714 β = 90 c = 200.994 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 CCD ADSC QUANTUM 210 2005-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 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 3.51 40.38 0.175 6.6 3.6 25439 2
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 1L8Q RESIDUES 77 TO 240 3.51 30 24077 1293 84.56 0.26738 0.26572 0.2463 0.29796 0.2496 RANDOM 94.374
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] -6.72 12.85 -6.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.615 r_dihedral_angle_3_deg 19.348 r_dihedral_angle_4_deg 15.755 r_mcangle_it 11.575 r_mcbond_it 8.768 r_dihedral_angle_1_deg 6.367 r_scangle_it 4.06 r_scbond_it 3.175 r_angle_refined_deg 1.001 r_nbtor_refined 0.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.615 r_dihedral_angle_3_deg 19.348 r_dihedral_angle_4_deg 15.755 r_mcangle_it 11.575 r_mcbond_it 8.768 r_dihedral_angle_1_deg 6.367 r_scangle_it 4.06 r_scbond_it 3.175 r_angle_refined_deg 1.001 r_nbtor_refined 0.322 r_nbd_refined 0.269 r_symmetry_vdw_refined 0.257 r_xyhbond_nbd_refined 0.186 r_symmetry_hbond_refined 0.171 r_metal_ion_refined 0.127 r_chiral_restr 0.075 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other 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 10437 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data scaling PHASER phasing