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ABC transporter-associated periplasmic binding protein DppA from Helicobacter pylori in complex with peptide STSA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5F1Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 23% PEG 3350, 0.25 M tri-ammonium citrate
Crystal Properties Matthews coefficient Solvent content 2.66 53.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.12 α = 90 b = 75.77 β = 90 c = 128.37 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 ADSC QUANTUM 210r 2018-04-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9184 Australian Synchrotron MX1
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 1.45 38.92 86.1 0.093 0.115 0.065 0.992 6.2 2.5 95404
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 1.45 1.47 84.6 0.393 0.497 0.297 0.751 2.4
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 5F1Q 1.45 38.92 90711 4656 85.64 0.1483 0.1469 0.1751 0.1854 RANDOM 11.887
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 r_dihedral_angle_2_deg 38.529 r_dihedral_angle_4_deg 17.765 r_dihedral_angle_3_deg 12.462 r_dihedral_angle_1_deg 6.417 r_angle_refined_deg 2.192 r_angle_other_deg 1.116 r_chiral_restr 0.138 r_gen_planes_refined 0.014 r_bond_refined_d 0.012 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.529 r_dihedral_angle_4_deg 17.765 r_dihedral_angle_3_deg 12.462 r_dihedral_angle_1_deg 6.417 r_angle_refined_deg 2.192 r_angle_other_deg 1.116 r_chiral_restr 0.138 r_gen_planes_refined 0.014 r_bond_refined_d 0.012 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4146 Nucleic Acid Atoms Solvent Atoms 875 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing