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Structure of the C-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 5BU1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1 M HEPES, 25% (w/v) PEG3350, 5 mM ADP
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.867 α = 89.87 b = 69.707 β = 72.3 c = 77.027 γ = 70.31
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 2014-03-14 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 2.1 50 95 0.098 11.3 2.6 57062 54209
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 2.1 2.14 78.3 0.435 1.7 2.5
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 5BU1 2.11 34 54209 2884 94.28 0.23123 0.22898 0.2315 0.27307 0.2768 RANDOM 37.641
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] 4.75 -1.13 -1.43 -1.88 -0.5 -3.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.213 r_dihedral_angle_4_deg 24.339 r_dihedral_angle_3_deg 19.308 r_dihedral_angle_1_deg 5.126 r_long_range_B_refined 4.839 r_mcangle_it 2.415 r_scbond_it 1.897 r_mcbond_it 1.511 r_angle_refined_deg 1.212 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.213 r_dihedral_angle_4_deg 24.339 r_dihedral_angle_3_deg 19.308 r_dihedral_angle_1_deg 5.126 r_long_range_B_refined 4.839 r_mcangle_it 2.415 r_scbond_it 1.897 r_mcbond_it 1.511 r_angle_refined_deg 1.212 r_chiral_restr 0.084 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_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 9218 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 141
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling ARP model building Coot model building