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Structure of the DnaG primase catalytic domain bound to ssDNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DDE PDB ENTRY 1DDE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 292 21% PEG 4000, 100 mM ammonium acetate, 50 mM sodium acetate (pH 5.0), VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.33 47.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.829 α = 90 b = 136.829 β = 90 c = 71.071 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 110 CCD ADSC QUANTUM 210 2006-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.111 ALS 8.3.1
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 2.35 50 95.7 0.065 14.8 3.3 31918 30546 2 53.5
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 2.35 2.43 97.3 0.458 2.2 2.9 3073
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) 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 1DDE 2.35 40 2 30166 28547 1519 94.63 0.21398 0.21185 0.2159 0.25443 0.262 RANDOM 42.878
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] 0.83 0.42 0.83 -1.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.819 r_dihedral_angle_4_deg 15.974 r_dihedral_angle_3_deg 14.446 r_dihedral_angle_1_deg 6.269 r_scangle_it 2.724 r_scbond_it 1.771 r_mcangle_it 1.274 r_angle_refined_deg 1.185 r_angle_other_deg 0.945 r_mcbond_it 0.807
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.819 r_dihedral_angle_4_deg 15.974 r_dihedral_angle_3_deg 14.446 r_dihedral_angle_1_deg 6.269 r_scangle_it 2.724 r_scbond_it 1.771 r_mcangle_it 1.274 r_angle_refined_deg 1.185 r_angle_other_deg 0.945 r_mcbond_it 0.807 r_symmetry_vdw_other 0.258 r_symmetry_vdw_refined 0.24 r_nbd_refined 0.213 r_nbd_other 0.209 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.179 r_symmetry_hbond_refined 0.13 r_mcbond_other 0.126 r_nbtor_other 0.083 r_chiral_restr 0.064 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4968 Nucleic Acid Atoms 240 Solvent Atoms 146 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing