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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 3.5 293 Crystallized in 3.5M NaCl, 0.1M citrate buffer pH 3.5.
Soaked in 50% (w/v) PEG 6000, BSA 0.8 mg/ml, 0.1M citrate buffer pH 3.5
(5 microliter drop for 3 hours)
Crystal Properties Matthews coefficient Solvent content 3.35 63.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.72 α = 90 b = 126.72 β = 90 c = 126.72 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 2019-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.976 MAX IV BioMAX
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 2.6 73.2 92.7 0.137 0.993 8.08 4.56 10394
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 2.6 2.67 97.1 0.571 0.799
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 2.6 73.2 9820 573 93.03 0.19867 0.19504 0.2039 0.26217 0.2631 RANDOM 39.714
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 12.172 r_dihedral_angle_1_deg 7.559 r_long_range_B_other 6.052 r_long_range_B_refined 6.041 r_mcangle_it 4.16 r_mcangle_other 4.158 r_scangle_other 3.845 r_dihedral_angle_2_deg 3.688 r_mcbond_it 2.662 r_mcbond_other 2.661
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.172 r_dihedral_angle_1_deg 7.559 r_long_range_B_other 6.052 r_long_range_B_refined 6.041 r_mcangle_it 4.16 r_mcangle_other 4.158 r_scangle_other 3.845 r_dihedral_angle_2_deg 3.688 r_mcbond_it 2.662 r_mcbond_other 2.661 r_scbond_it 2.434 r_scbond_other 2.432 r_angle_refined_deg 1.381 r_angle_other_deg 0.406 r_bond_refined_d 0.121 r_chiral_restr 0.05 r_gen_planes_refined 0.008 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 44 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing