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Crystal structure of Paenibacillus sp. 598K alpha-1,6-glucosyltransferase complexed with acarbose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5X7O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.6 293 1.5 M magnesium sulfate,
0.1 M MES buffer pH 6.6
Crystal Properties Matthews coefficient Solvent content 3.05 59.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.287 α = 90 b = 271.517 β = 90 c = 133.63 γ = 90
Symmetry Space Group C 2 2 21
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 2013-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0000 Photon Factory AR-NE3A
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 2.4 200 99.9 0.123 21.3 14.2 129967 38.773
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 2.4 2.49 100 0.938 3.4 13.4
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 5X7O 2.4 152.48 120149 6373 97.08 0.18313 0.18027 0.1895 0.23695 0.2422 RANDOM 42.319
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] 0.9 -4.63 3.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.382 r_dihedral_angle_4_deg 17.687 r_dihedral_angle_3_deg 13.974 r_dihedral_angle_1_deg 7.215 r_long_range_B_refined 5.859 r_long_range_B_other 5.849 r_scangle_other 4.563 r_mcangle_it 3.97 r_mcangle_other 3.97 r_scbond_it 3.193
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.382 r_dihedral_angle_4_deg 17.687 r_dihedral_angle_3_deg 13.974 r_dihedral_angle_1_deg 7.215 r_long_range_B_refined 5.859 r_long_range_B_other 5.849 r_scangle_other 4.563 r_mcangle_it 3.97 r_mcangle_other 3.97 r_scbond_it 3.193 r_scbond_other 3.193 r_mcbond_it 2.833 r_mcbond_other 2.833 r_angle_refined_deg 1.666 r_angle_other_deg 0.996 r_chiral_restr 0.094 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 19202 Nucleic Acid Atoms Solvent Atoms 794 Heterogen Atoms 516
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing