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Crystal structure of the nucleotide-binding domain (NBD) of LipB, a ABC transporter subunit of a type I secretion system
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277 1.4M K2HPO4, 0.6M NaH2PO4, 0.1M imidazole pH 8.0, 0.2M NaCl
Crystal Properties Matthews coefficient Solvent content 3.33 63.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.302 α = 90 b = 61.298 β = 104.03 c = 88.313 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 173 CCD MARMOSAIC 225 mm CCD 2010-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 2.65 50 98.7 0.081 18.05 4.6 21754
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 2.65 2.7 90.5 0.497 1.53 3.8
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 MOLECULAR REPLACEMENT THROUGHOUT 2.65 35.63 20626 1116 98.35 0.20752 0.20447 0.2141 0.26133 0.2563 RANDOM 56.357
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] 0.04 0.03 -0.05 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.943 r_dihedral_angle_3_deg 20.55 r_dihedral_angle_4_deg 20.439 r_long_range_B_refined 14.646 r_long_range_B_other 14.645 r_scangle_other 11.6 r_dihedral_angle_1_deg 9.375 r_mcangle_other 9.002 r_mcangle_it 8.998 r_scbond_it 7.802
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.943 r_dihedral_angle_3_deg 20.55 r_dihedral_angle_4_deg 20.439 r_long_range_B_refined 14.646 r_long_range_B_other 14.645 r_scangle_other 11.6 r_dihedral_angle_1_deg 9.375 r_mcangle_other 9.002 r_mcangle_it 8.998 r_scbond_it 7.802 r_scbond_other 7.801 r_mcbond_it 6.462 r_mcbond_other 6.444 r_angle_refined_deg 0.713 r_angle_other_deg 0.526 r_chiral_restr 0.049 r_gen_planes_refined 0.012 r_bond_refined_d 0.004 r_gen_planes_other 0.002 r_bond_other_d 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 3464 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing