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Crystal structure of the outer membrane channel DcaP of Acinetobacter baumannii
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 8.5% MPD,
8.5% PEG 1000,
8.5% PEG 3350,
0.02 M sodium formate,
0.02 M sodium citrate,
0.02 M sodium oxamate,
0.02 M ammonium acetate,
0.02 M sodium potassium tartrate,
0.05 M MES,
0.05 M imidazole pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.55 51.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.847 α = 90 b = 108.382 β = 90 c = 216.202 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 2015-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97926 Diamond I03
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 48.44 97.5 0.1 6 2.9 125363
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.24 99.1 0.739 1.4 3
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.2 108.1 122906 2362 97.13 0.20065 0.20001 0.2078 0.23362 0.2404 RANDOM 38.879
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] -0.08 -0.62 0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.066 r_dihedral_angle_4_deg 18.337 r_dihedral_angle_3_deg 15.366 r_dihedral_angle_1_deg 7.957 r_long_range_B_refined 5.302 r_long_range_B_other 5.274 r_scangle_other 3.256 r_scbond_it 2.18 r_scbond_other 2.18 r_mcangle_it 2.166
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.066 r_dihedral_angle_4_deg 18.337 r_dihedral_angle_3_deg 15.366 r_dihedral_angle_1_deg 7.957 r_long_range_B_refined 5.302 r_long_range_B_other 5.274 r_scangle_other 3.256 r_scbond_it 2.18 r_scbond_other 2.18 r_mcangle_it 2.166 r_mcangle_other 2.166 r_angle_refined_deg 2.041 r_mcbond_it 1.45 r_mcbond_other 1.45 r_angle_other_deg 1.063 r_chiral_restr 0.126 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.002 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 15906 Nucleic Acid Atoms Solvent Atoms 694 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling AutoSol phasing