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Crystal structure of Paenibacillus sp. 598K alpha-1,6-glucosyltransferase complexed with isomaltohexaose
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
Crystal Properties Matthews coefficient Solvent content 3.05 59.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.333 α = 90 b = 271.26 β = 90 c = 133.928 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 1.95 200 99.9 0.078 33.2 14.5 245688 24.93
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 1.95 2.02 99.8 0.567 6 13.2
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 1.95 152.46 224154 11854 97.41 0.17981 0.17832 0.1884 0.20779 0.2156 RANDOM 33.004
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] 1.72 -3.76 2.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.044 r_dihedral_angle_4_deg 16.852 r_dihedral_angle_3_deg 12.132 r_dihedral_angle_1_deg 6.483 r_long_range_B_refined 4.592 r_long_range_B_other 4.551 r_scangle_other 2.988 r_mcangle_it 2.275 r_mcangle_other 2.275 r_scbond_it 1.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.044 r_dihedral_angle_4_deg 16.852 r_dihedral_angle_3_deg 12.132 r_dihedral_angle_1_deg 6.483 r_long_range_B_refined 4.592 r_long_range_B_other 4.551 r_scangle_other 2.988 r_mcangle_it 2.275 r_mcangle_other 2.275 r_scbond_it 1.97 r_scbond_other 1.968 r_mcbond_it 1.551 r_mcbond_other 1.55 r_angle_refined_deg 1.331 r_angle_other_deg 0.903 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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 19202 Nucleic Acid Atoms Solvent Atoms 1652 Heterogen Atoms 596
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing