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X-ray crystal structure of a periplasmic oligopeptide-binding protein/Oligopeptide ABC transporter(OppAIV) from Borrelia burgdorferi
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OLA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.12 289 Morpheus G4: 1x MORPHEUS PRECIPITANTS, 1x MORPHEUS CARBOHYDRATES, 1x MORPHEUS BUFFER ph 6.12, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.22 44.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.75 α = 90 b = 103.58 β = 90 c = 104.81 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 315r 2012-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1.000 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.2 50 98.643 0.1 14.74 4.78 55780 55023 -3 -3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1OLA 2.2 19.86 52943 52223 2800 98.64 0.17425 0.17425 0.17175 0.1788 0.22046 0.2253 RANDOM 27.594
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] 1.84 -0.96 -0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.805 r_dihedral_angle_3_deg 14.115 r_dihedral_angle_4_deg 12.758 r_dihedral_angle_1_deg 6.019 r_angle_refined_deg 1.448 r_angle_other_deg 0.803 r_chiral_restr 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.805 r_dihedral_angle_3_deg 14.115 r_dihedral_angle_4_deg 12.758 r_dihedral_angle_1_deg 6.019 r_angle_refined_deg 1.448 r_angle_other_deg 0.803 r_chiral_restr 0.081 r_bond_refined_d 0.011 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it 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 7965 Nucleic Acid Atoms Solvent Atoms 461 Heterogen Atoms
Software Software Software Name Purpose PHASER phasing REFMAC refinement XSCALE data scaling