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X-ray crystal structure of LsAA9A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ACH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 3.5M NaCl, 0.1M citrate buffer pH 3.5 in 96-wells MRC-2 plates with 70 microliter of reservoirs and 0.3 microliter drops
Crystal Properties Matthews coefficient Solvent content 3.27 62.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.61 α = 90 b = 125.61 β = 90 c = 125.61 γ = 90
Symmetry Space Group P 41 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 EIGER X 16M 2019-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.805 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 2.7 50 97.5 0.077 0.994 15.52 3.88 9557
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.77 97.3 0.212 0.973 3.64
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 FOURIER SYNTHESIS THROUGHOUT 2.7 44.45 9049 508 97.45 0.17966 0.17632 0.1868 0.23848 0.2415 RANDOM 22.029
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 12.972 r_dihedral_angle_1_deg 6.878 r_long_range_B_refined 5.75 r_long_range_B_other 5.73 r_dihedral_angle_2_deg 4.979 r_scangle_other 3.489 r_mcangle_other 2.638 r_mcangle_it 2.635 r_scbond_other 2.212 r_scbond_it 2.207
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.972 r_dihedral_angle_1_deg 6.878 r_long_range_B_refined 5.75 r_long_range_B_other 5.73 r_dihedral_angle_2_deg 4.979 r_scangle_other 3.489 r_mcangle_other 2.638 r_mcangle_it 2.635 r_scbond_other 2.212 r_scbond_it 2.207 r_mcbond_other 1.599 r_mcbond_it 1.597 r_angle_refined_deg 1.404 r_angle_other_deg 0.47 r_chiral_restr 0.057 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 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 1788 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing