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Crystal structure of Helicobacter pylori DnaG Primase C terminal domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 289 PEG 5000 MME, NaCl, pH 7.4, vapor diffusion, hanging drop, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.82 32.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.883 α = 90 b = 61.455 β = 90 c = 82.421 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 MARMOSAIC 225 mm CCD bent collimating mirror and toroid 2010-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97860 ESRF BM14
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 1.78 50 99.5 0.067 42.3 6.7 24493 -3
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 1.78 1.81 94.2 0.332 3.8 4.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 SAD THROUGHOUT 1.78 49.27 24598 23200 1250 99.59 0.19779 0.19502 0.1983 0.24929 0.2514 RANDOM 23.766
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] -0.24 1.06 -0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.736 r_dihedral_angle_3_deg 15.638 r_dihedral_angle_4_deg 15.477 r_scangle_it 6.855 r_dihedral_angle_1_deg 5.484 r_scbond_it 4.318 r_mcangle_it 2.598 r_angle_refined_deg 2.184 r_mcbond_it 1.467 r_chiral_restr 0.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.736 r_dihedral_angle_3_deg 15.638 r_dihedral_angle_4_deg 15.477 r_scangle_it 6.855 r_dihedral_angle_1_deg 5.484 r_scbond_it 4.318 r_mcangle_it 2.598 r_angle_refined_deg 2.184 r_mcbond_it 1.467 r_chiral_restr 0.126 r_bond_refined_d 0.019 r_gen_planes_refined 0.012 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1993 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 16
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction DNA data collection SHELXS phasing