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Crystal structure of Klebsiella pneumoniae K1 capsule-specific polysaccharide lyase in complex with products
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 15% (W/V) PEG 4000, 0.2 M IMIDAZOLE MALATE, PH 6.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 2.46 50.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.626 α = 80.4 b = 100.991 β = 70.48 c = 125.38 γ = 83.99
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 MX300HE 2013-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1.0 NSRRC BL15A1
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 1.46 30 94.4 0.032 19.84 2 673887 2
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 1.46 1.51 92.9 0.243 2.14 2
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 MAD THROUGHOUT 1.46 30 640111 33731 94.2 0.116 0.114 0.148 0.1606 RANDOM 18
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] 0.52 -0.61 -0.07 -0.21 0.56 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.98 r_sphericity_free 29.116 r_dihedral_angle_4_deg 17.211 r_dihedral_angle_3_deg 10.518 r_sphericity_bonded 9.106 r_dihedral_angle_1_deg 7.109 r_rigid_bond_restr 3.335 r_angle_other_deg 2.52 r_angle_refined_deg 1.514 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.98 r_sphericity_free 29.116 r_dihedral_angle_4_deg 17.211 r_dihedral_angle_3_deg 10.518 r_sphericity_bonded 9.106 r_dihedral_angle_1_deg 7.109 r_rigid_bond_restr 3.335 r_angle_other_deg 2.52 r_angle_refined_deg 1.514 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_gen_planes_other 0.006 r_bond_other_d 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28933 Nucleic Acid Atoms Solvent Atoms 4887 Heterogen Atoms 534
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction