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Crystal Structure of the putative amino acid-binding periplasmic ABC transporter protein from Candidatus Liberibacter asiaticus in complex with Cysteine
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 = 45.791 α = 90 b = 87.049 β = 90 c = 122.164 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 2.05 70.89 99.8 0.147 0.147 0.071 0.994 8.5 5.2 31433 35
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.12 99.7 0.452 0.702 2.1 5.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 2.05 36.885 1.35 31364 1503 99.71 0.2001 0.1971 0.202 0.2583 0.2591 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.772 f_angle_d 0.886 f_chiral_restr 0.054 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3760 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 149
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling MoRDa phasing