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Crystal Structure of putative amino acid binding periplasmic ABC transporter protein from Candidatus Liberibacter asiaticus in complex with cystine
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
Crystal Properties Matthews coefficient Solvent content 2.22 44.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.16 α = 90 b = 86.78 β = 90 c = 122.25 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 2017-11-03 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) Rrim I (All) 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 1.56 70.76 99.8 0.033 0.038 0.018 0.999 20.1 4.5 70624 26.46
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 1.56 1.587 99.7 0.683 0.781 0.5 0.809 2.2 4.2
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 1.56 70.76 67009 3614 99.78 0.18731 0.18546 0.1858 0.22131 0.2217 RANDOM 32.021
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] 0.92 0.65 -1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.434 r_dihedral_angle_4_deg 21.14 r_dihedral_angle_3_deg 15.32 r_dihedral_angle_1_deg 9.567 r_long_range_B_refined 8.095 r_scbond_it 4.144 r_mcangle_it 3.39 r_mcbond_it 2.681 r_angle_refined_deg 2.091 r_chiral_restr 0.151
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.434 r_dihedral_angle_4_deg 21.14 r_dihedral_angle_3_deg 15.32 r_dihedral_angle_1_deg 9.567 r_long_range_B_refined 8.095 r_scbond_it 4.144 r_mcangle_it 3.39 r_mcbond_it 2.681 r_angle_refined_deg 2.091 r_chiral_restr 0.151 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other 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 292 Heterogen Atoms 156
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling MoRDa phasing