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X-ray crystal structure of LsAA9B (deglycosylated form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EJA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 16%(w/v) MPD (racemic)
16%(w/v) PEG 1000
16%(w/v) PEG 3350
20 mM of Glutamate, Alanine, Glycine, Lysine, and Serine (some racemic).
30 mM of each of NaNO3; Na2HPO4; (NH4)2SO4
100 mM Imidazole/MES 0.1 M (pH6.5)
Crystal Properties Matthews coefficient Solvent content 2.17 43.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.08 α = 90 b = 72.99 β = 90 c = 79.06 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 CCD MARMOSAIC 225 mm CCD Collimating mirror , double-crystal monochromator (DCM), focusing mirror 2014-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 1.0000 MAX II I911-3
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 1.6 20 98.5 0.084 0.998 14.39 5.81 27139
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 1.6 1.7 91.7 0.82 0.766 1.94 3.59
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 3EJA 1.6 20 25753 1386 98.51 0.15476 0.15171 0.1517 0.21142 0.2123 RANDOM 18.437
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] -0.23 1.69 -1.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.544 r_dihedral_angle_4_deg 23.654 r_sphericity_bonded 15.84 r_dihedral_angle_3_deg 11.707 r_dihedral_angle_1_deg 6.019 r_rigid_bond_restr 5.376 r_long_range_B_refined 3.102 r_long_range_B_other 3.102 r_scangle_other 2.151 r_scbond_it 1.699
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.544 r_dihedral_angle_4_deg 23.654 r_sphericity_bonded 15.84 r_dihedral_angle_3_deg 11.707 r_dihedral_angle_1_deg 6.019 r_rigid_bond_restr 5.376 r_long_range_B_refined 3.102 r_long_range_B_other 3.102 r_scangle_other 2.151 r_scbond_it 1.699 r_scbond_other 1.697 r_mcangle_other 1.604 r_mcangle_it 1.598 r_angle_refined_deg 1.475 r_mcbond_other 1.254 r_mcbond_it 1.234 r_angle_other_deg 0.945 r_chiral_restr 0.063 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1645 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 89
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection XDS data reduction XSCALE data scaling MOLREP phasing Coot model building