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Structure of the N-terminal domain of lpg1496 from Legionella pneumophila in complex with nucleotide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5BTW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2 M sodium chloride, 0.1 M Bis-Tris pH6.5, 25% (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 1.83 32.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.622 α = 90 b = 57.446 β = 93.32 c = 63.779 γ = 90
Symmetry Space Group P 1 21 1
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 2014-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.9770 CHESS A1
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 1.75 50 89.2 0.076 39 6.6 14063 12544
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 1.75 1.78 92.3 0.497 5.3 6.4
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 5BTW 2.1 30 12544 654 94.46 0.2404 0.23763 0.2403 0.29159 0.2952 RANDOM 33.276
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] -2.8 0.38 -1.7 4.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.2 r_dihedral_angle_3_deg 16.839 r_dihedral_angle_1_deg 10.665 r_long_range_B_refined 4.543 r_mcangle_it 2.126 r_scbond_it 1.648 r_angle_refined_deg 1.643 r_mcbond_it 1.409 r_chiral_restr 0.104 r_bond_refined_d 0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.2 r_dihedral_angle_3_deg 16.839 r_dihedral_angle_1_deg 10.665 r_long_range_B_refined 4.543 r_mcangle_it 2.126 r_scbond_it 1.648 r_angle_refined_deg 1.643 r_mcbond_it 1.409 r_chiral_restr 0.104 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_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_it r_scangle_other 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 2057 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement PHASER phasing Coot model building HKL-2000 data reduction HKL-2000 data scaling