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Structure of the N-terminal domain of lpg1496 from Legionella pneumophila
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5BTY PDB entry 5BTY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2 M sodium formate, 20% (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 27.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.41 α = 90 b = 56.92 β = 91.18 c = 60.184 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 2014-03-12 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 1.2 50 92.7 0.056 43.9 7.7 65120 60366
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 1.2 1.22 84.3 0.567 2.8 6
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 5BTY 1.2 50 60366 3018 92.51 0.1586 0.1575 0.1633 0.17952 0.1833 RANDOM 14.582
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] -0.33 0.03 -0.19 0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.783 r_sphericity_free 12.844 r_dihedral_angle_3_deg 12.16 r_sphericity_bonded 7.382 r_dihedral_angle_1_deg 5.756 r_long_range_B_refined 2.46 r_scbond_it 2.331 r_mcangle_it 1.531 r_angle_refined_deg 1.462 r_mcbond_it 1.152
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.783 r_sphericity_free 12.844 r_dihedral_angle_3_deg 12.16 r_sphericity_bonded 7.382 r_dihedral_angle_1_deg 5.756 r_long_range_B_refined 2.46 r_scbond_it 2.331 r_mcangle_it 1.531 r_angle_refined_deg 1.462 r_mcbond_it 1.152 r_rigid_bond_restr 1.083 r_chiral_restr 0.105 r_bond_refined_d 0.012 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2064 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling ARP model building Coot model building