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Crystal structure of the Legionella pneumoppila LapA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GNE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.5 293 0.1M MES pH 5.5, 25% (w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.24 45.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.597 α = 90 b = 99.556 β = 90 c = 104.012 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 PIXEL DECTRIS PILATUS3 6M 2017-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
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 1.87 99.55 100 0.063 12.5 6.5 66414
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.87 1.92 100 1.2 3.7 6.2
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 5GNE 1.87 99.56 62722 3366 99.6 0.19471 0.1924 0.2072 0.23765 0.242 RANDOM 40.644
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] 0.11 0.39 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.971 r_dihedral_angle_4_deg 17.079 r_dihedral_angle_3_deg 15.826 r_dihedral_angle_1_deg 6.425 r_long_range_B_refined 5.93 r_long_range_B_other 5.899 r_scangle_other 3.625 r_mcangle_it 2.649 r_mcangle_other 2.649 r_scbond_it 2.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.971 r_dihedral_angle_4_deg 17.079 r_dihedral_angle_3_deg 15.826 r_dihedral_angle_1_deg 6.425 r_long_range_B_refined 5.93 r_long_range_B_other 5.899 r_scangle_other 3.625 r_mcangle_it 2.649 r_mcangle_other 2.649 r_scbond_it 2.305 r_scbond_other 2.305 r_angle_refined_deg 2.045 r_mcbond_other 1.749 r_mcbond_it 1.748 r_angle_other_deg 1.152 r_chiral_restr 0.149 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5682 Nucleic Acid Atoms Solvent Atoms 313 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement Aimless data reduction SCALA data scaling PHASER phasing