☰ Navigation Tabs
Crystal structure of an ABC transporter related protein from Burkholderia pseudomallei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WBS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 296 Protein buffer: 50 mM HEPES pH 7.0, 150 mM NaCl, 5 mM MgCl2, 500 uM ATP
Crystallisation condition:
0.2 M MgCl2, 0.1 M Tris-HCL pH 8.5, 30 % w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.15 42.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.787 α = 90 b = 74.228 β = 90 c = 124.378 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 S 6M 2017-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.968580 Diamond I24
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 2.4 29.49 97 0.119 0.159 0.103 0.982 10.2 3.8 19107 22.5
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 2.4 2.49 98 0.792 0.941 0.496 0.487 5.8 3.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4WBS 2.4 29.51 18145 923 96.5 0.20817 0.20486 0.2083 0.26999 0.2665 RANDOM 28.814
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] -2.13 1.62 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.387 r_dihedral_angle_4_deg 21.314 r_dihedral_angle_3_deg 16.579 r_long_range_B_refined 6.772 r_long_range_B_other 6.763 r_dihedral_angle_1_deg 6.6 r_scangle_other 4.412 r_mcangle_it 3.826 r_mcangle_other 3.826 r_scbond_it 2.591
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.387 r_dihedral_angle_4_deg 21.314 r_dihedral_angle_3_deg 16.579 r_long_range_B_refined 6.772 r_long_range_B_other 6.763 r_dihedral_angle_1_deg 6.6 r_scangle_other 4.412 r_mcangle_it 3.826 r_mcangle_other 3.826 r_scbond_it 2.591 r_scbond_other 2.59 r_mcbond_it 2.263 r_mcbond_other 2.257 r_angle_refined_deg 1.253 r_angle_other_deg 0.85 r_chiral_restr 0.062 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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 3777 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing