☰ Navigation Tabs
1.93 Angstrom resolution crystal structure of a pullulanase-specific type II secretion system integral cytoplasmic membrane protein GspL (C-terminal fragment; residues 309-397) from Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 protein: 9.7 mg/mL 10 mM Tris-HCl pH 8.3
crystallization: The Classics II Suite conditions E7 (#55): 0.05 M MgCl2, 0.1 M HEPES pH 7.5, 30 % (v/v) PEG 550 MME
cryo: crystallization conditions
Crystal Properties Matthews coefficient Solvent content 1.87 34.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.375 α = 90 b = 51.284 β = 90 c = 117.021 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 MARMOSAIC 300 mm CCD C(111) 2015-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 1.93 30 99.9 0.069 58.1 14.4 23407 -3 28.7
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 1.93 1.96 100 0.588 5.7 14.7
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 1.93 26.44 22151 1203 99.77 0.22899 0.22621 0.2309 0.28137 0.2863 RANDOM 45.834
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] 3.18 -0.52 -2.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.516 r_dihedral_angle_4_deg 13.686 r_dihedral_angle_3_deg 9.642 r_dihedral_angle_1_deg 3.445 r_angle_refined_deg 1.65 r_angle_other_deg 1.302 r_chiral_restr 0.094 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.516 r_dihedral_angle_4_deg 13.686 r_dihedral_angle_3_deg 9.642 r_dihedral_angle_1_deg 3.445 r_angle_refined_deg 1.65 r_angle_other_deg 1.302 r_chiral_restr 0.094 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.006 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_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2412 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing Coot model building