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Crystal structur of Lpg1618(R215F) from Legionella pneumophila
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 289 0.1M Tris-HCl pH7.2, 2.5M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.69 54.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 156.189 α = 90 b = 156.189 β = 90 c = 156.189 γ = 90
Symmetry Space Group P 43 3 2
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 PILATUS 6M 2024-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97853 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.9 50 100 0.998 25 72.1 51671
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.95 0.723 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.9 20 48972 2502 99.73 0.17056 0.16972 0.1745 0.18682 0.2003 RANDOM 23.067
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.489 r_long_range_B_refined 8.972 r_long_range_B_other 8.972 r_scangle_other 6.583 r_dihedral_angle_1_deg 5.545 r_scbond_it 4.524 r_scbond_other 4.523 r_mcangle_other 4.063 r_mcangle_it 4.062 r_mcbond_it 3.182
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.489 r_long_range_B_refined 8.972 r_long_range_B_other 8.972 r_scangle_other 6.583 r_dihedral_angle_1_deg 5.545 r_scbond_it 4.524 r_scbond_other 4.523 r_mcangle_other 4.063 r_mcangle_it 4.062 r_mcbond_it 3.182 r_mcbond_other 3.182 r_angle_refined_deg 1.489 r_dihedral_angle_2_deg 0.87 r_angle_other_deg 0.753 r_chiral_restr 0.074 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_gen_planes_other 0.005 r_bond_other_d 0.001 r_dihedral_angle_4_deg 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 3970 Nucleic Acid Atoms Solvent Atoms 538 Heterogen Atoms 102
Software Software Software Name Purpose REFMAC refinement autoPX data reduction SCALA data scaling MOLREP phasing