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Crystal Structure of putative amino acid binding periplasmic ABC transporter protein from Candidatus Liberibacter asiaticus in complex with Arginine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YLN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277 2M Ammonium sulphate, 0.1M Sodium acetate trihydrate pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.31 46.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.342 α = 90 b = 86 β = 90 c = 123.832 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 IMAGE PLATE MARRESEARCH 2017-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 70.64 98.6 0.15 9.5 4.2 15666 41.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.64 96.9 0.8 1.23 3.1
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 2YLN 2.6 70.64 14811 826 98.71 0.20509 0.20018 0.2048 0.29013 0.289 RANDOM 40.787
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] 0.31 0.13 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.662 r_dihedral_angle_4_deg 18.314 r_dihedral_angle_3_deg 18.075 r_dihedral_angle_1_deg 7.467 r_long_range_B_other 6.567 r_long_range_B_refined 6.566 r_scangle_other 4.48 r_mcangle_it 4.179 r_mcangle_other 4.178 r_scbond_it 2.896
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.662 r_dihedral_angle_4_deg 18.314 r_dihedral_angle_3_deg 18.075 r_dihedral_angle_1_deg 7.467 r_long_range_B_other 6.567 r_long_range_B_refined 6.566 r_scangle_other 4.48 r_mcangle_it 4.179 r_mcangle_other 4.178 r_scbond_it 2.896 r_scbond_other 2.896 r_mcbond_it 2.696 r_mcbond_other 2.695 r_angle_refined_deg 1.618 r_angle_other_deg 0.843 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3760 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MoRDa phasing