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Crystal structure of putative amino acid binding periplasmic ABC transporter protein from Candidatus Liberibacter asiaticus bound with citrate
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 20% PEG 550, 0.1 M Sodium Citrate pH 5.0
Crystal Properties Matthews coefficient Solvent content 2.21 44.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.07 α = 90 b = 86.96 β = 90 c = 121.8 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 PIXEL DECTRIS PILATUS3 6M 2018-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.976251 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 1.857 70.773 99.9 0.142 0.05 0.997 12.5 8.9 42127 25.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.857 1.889 100 1.14 1.213 0.407 0.664 2.2 8.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2YLN 1.86 70.77 40111 2016 99.94 0.18826 0.18641 0.22517 0.2141 RANDOM 25.019
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] 0.88 0.45 -1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.296 r_dihedral_angle_1_deg 22.332 r_dihedral_angle_4_deg 19.935 r_dihedral_angle_3_deg 14.382 r_long_range_B_refined 6.78 r_long_range_B_other 6.756 r_scangle_other 4.566 r_scbond_it 2.997 r_scbond_other 2.995 r_mcangle_it 2.644
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.296 r_dihedral_angle_1_deg 22.332 r_dihedral_angle_4_deg 19.935 r_dihedral_angle_3_deg 14.382 r_long_range_B_refined 6.78 r_long_range_B_other 6.756 r_scangle_other 4.566 r_scbond_it 2.997 r_scbond_other 2.995 r_mcangle_it 2.644 r_mcangle_other 2.643 r_angle_refined_deg 1.807 r_mcbond_it 1.796 r_mcbond_other 1.796 r_angle_other_deg 0.889 r_chiral_restr 0.116 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 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 261 Heterogen Atoms 219
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling MoRDa phasing