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Crystal Structure of Paenibacillus sp. 598K cycloisomaltooligosaccharide glucanotransferase complexed with cycloisomaltoheptaose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5X7G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 25% PEG3350, 12% Tacsimate
Crystal Properties Matthews coefficient Solvent content 2.81 56.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.844 α = 90 b = 112.844 β = 90 c = 122.275 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 270 2015-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.6 100 99.9 0.109 0.4 10.9 20.5 28297
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.69 100 0.922 0.214 3.3
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 5X7G 2.6 97.73 26895 1324 99.63 0.15781 0.15509 0.164 0.21456 0.2187 RANDOM 44.404
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] 1.35 0.67 1.35 -4.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.507 r_dihedral_angle_4_deg 18.583 r_dihedral_angle_3_deg 15.008 r_long_range_B_other 7.937 r_long_range_B_refined 7.935 r_dihedral_angle_1_deg 7.301 r_scangle_other 5.352 r_mcangle_it 4.616 r_mcangle_other 4.615 r_scbond_it 3.427
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.507 r_dihedral_angle_4_deg 18.583 r_dihedral_angle_3_deg 15.008 r_long_range_B_other 7.937 r_long_range_B_refined 7.935 r_dihedral_angle_1_deg 7.301 r_scangle_other 5.352 r_mcangle_it 4.616 r_mcangle_other 4.615 r_scbond_it 3.427 r_scbond_other 3.424 r_mcbond_it 2.947 r_mcbond_other 2.945 r_angle_refined_deg 1.638 r_angle_other_deg 0.995 r_chiral_restr 0.091 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 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 5541 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms 198
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing