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X-ray crystal structure of LsAA9B
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 6.5 294 20%(w/v) Polyethylene glycol monomethyl ether 500
10%(w/v) Polyethylene glycol 20.000
0.1 M Imidazole/MES (pH6.5)
0.02 M Glutamate, Alanine, Glycine, Lysine, and Serine (some racemic).
Crystal Properties Matthews coefficient Solvent content 2.16 42.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.19 α = 90 b = 72.48 β = 90 c = 78.56 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 2014-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 0.9900 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 99.6 0.108 0.998 14.07 7.83 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 98.5 0.678 0.764 2.74 6.01
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 19.93 25765 1384 99.6 0.13903 0.1367 0.1366 0.18219 0.1819 RANDOM 16.406
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] -0.41 0.26 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.843 r_dihedral_angle_4_deg 19.195 r_dihedral_angle_3_deg 10.468 r_sphericity_bonded 9.553 r_dihedral_angle_1_deg 6.495 r_rigid_bond_restr 4.561 r_long_range_B_refined 2.613 r_long_range_B_other 2.612 r_scangle_other 2.052 r_scbond_it 1.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.843 r_dihedral_angle_4_deg 19.195 r_dihedral_angle_3_deg 10.468 r_sphericity_bonded 9.553 r_dihedral_angle_1_deg 6.495 r_rigid_bond_restr 4.561 r_long_range_B_refined 2.613 r_long_range_B_other 2.612 r_scangle_other 2.052 r_scbond_it 1.52 r_scbond_other 1.519 r_angle_refined_deg 1.403 r_mcangle_it 1.354 r_mcangle_other 1.353 r_mcbond_other 0.98 r_mcbond_it 0.979 r_angle_other_deg 0.968 r_chiral_restr 0.06 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_gen_planes_other 0.001 r_bond_other_d 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 1640 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection XDS data reduction XSCALE data scaling MOLREP phasing Coot model building