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Crystal Structure of Paenibacillus sp. 598K cycloisomaltooligosaccharide glucanotransferase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WNK
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 = 113.68 α = 90 b = 113.68 β = 90 c = 121.635 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 2016-03-09 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 2.2 100 100 0.096 0.021 32.1 22.1 46942 33.366
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 2.2 2.28 100 0.848 0.184 4.9 22.1
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 3WNK 2.2 98.45 43870 2388 99.46 0.17666 0.17418 0.1828 0.22164 0.2252 RANDOM 45.419
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.111 r_dihedral_angle_4_deg 19.393 r_dihedral_angle_3_deg 14.178 r_dihedral_angle_1_deg 7.003 r_long_range_B_refined 6.672 r_long_range_B_other 6.67 r_scangle_other 4.757 r_mcangle_it 4.236 r_mcangle_other 4.235 r_scbond_it 3.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.111 r_dihedral_angle_4_deg 19.393 r_dihedral_angle_3_deg 14.178 r_dihedral_angle_1_deg 7.003 r_long_range_B_refined 6.672 r_long_range_B_other 6.67 r_scangle_other 4.757 r_mcangle_it 4.236 r_mcangle_other 4.235 r_scbond_it 3.125 r_scbond_other 3.122 r_mcbond_it 2.832 r_mcbond_other 2.831 r_angle_refined_deg 1.434 r_angle_other_deg 0.951 r_chiral_restr 0.089 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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 289 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing