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Crystal structure of periplasmic ABC transporter solute binding protein A7JW62 from Mannheimia haemolytica PHL213, Target EFI-511105, in complex with Myo-inositol
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 294 PROTEIN (10 MM HEPES PH 7.5, 5 MM DTT, 10 MM MYOINOSITOL); RESERVOIR: 0.1 M Na2HPO4:Citric Acid, PH 4.2, 0.2 M SODIUM CHLORIDE, 20% PEG8000; CRYOPROTECTION: RESERVOIR SOLUTION PLUS 20% GLUCOSE (VOL/VOL); VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.79 55.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.784 α = 90 b = 120.175 β = 90 c = 137.741 γ = 90
Symmetry Space Group C 2 2 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 RAYONIX MX225HE MIRRORS 2014-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.75 50 99.8 0.09 0.09 33.3 14.8 68349 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 100 0.97 0.97 3.5 14.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.75 50 68349 2148 99.24 0.15661 0.15566 0.18733 0.2124 RANDOM 35.649
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] 2.34 -0.45 -1.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.355 r_dihedral_angle_4_deg 18.244 r_dihedral_angle_3_deg 14.025 r_long_range_B_other 10.966 r_long_range_B_refined 10.955 r_scangle_other 10.452 r_scbond_it 8.67 r_scbond_other 8.656 r_dihedral_angle_1_deg 5.582 r_mcangle_other 5.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.355 r_dihedral_angle_4_deg 18.244 r_dihedral_angle_3_deg 14.025 r_long_range_B_other 10.966 r_long_range_B_refined 10.955 r_scangle_other 10.452 r_scbond_it 8.67 r_scbond_other 8.656 r_dihedral_angle_1_deg 5.582 r_mcangle_other 5.07 r_mcangle_it 5.046 r_mcbond_it 4.085 r_mcbond_other 4.022 r_angle_refined_deg 1.359 r_angle_other_deg 0.78 r_chiral_restr 0.082 r_bond_refined_d 0.01 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4376 Nucleic Acid Atoms Solvent Atoms 470 Heterogen Atoms 46
Software Software Software Name Purpose SHELX model building ARP/wARP model building REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling SHELX phasing