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Crystal structure of Paenibacillus sp. 598K alpha-1,6-glucosyltransferase, terbium derivative
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, 1 mM terbium chloride
Crystal Properties Matthews coefficient Solvent content 3.04 59.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.815 α = 90 b = 270.92 β = 90 c = 133.341 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 210 2011-11-03 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.64883,1.64955,1.60679 Photon Factory AR-NW12A
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 0.115 29.4 13.2 128840
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 2.44 100 0.861 2.9 12.1
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.4 151.54 113142 5912 92.42 0.18727 0.18458 0.1939 0.23871 0.2437 RANDOM 45.741
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] 3.06 -5.64 2.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.285 r_dihedral_angle_4_deg 18.525 r_dihedral_angle_3_deg 14.224 r_dihedral_angle_1_deg 7.265 r_long_range_B_refined 6.413 r_long_range_B_other 6.393 r_scangle_other 4.986 r_mcangle_it 4.428 r_mcangle_other 4.427 r_scbond_it 3.596
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.285 r_dihedral_angle_4_deg 18.525 r_dihedral_angle_3_deg 14.224 r_dihedral_angle_1_deg 7.265 r_long_range_B_refined 6.413 r_long_range_B_other 6.393 r_scangle_other 4.986 r_mcangle_it 4.428 r_mcangle_other 4.427 r_scbond_it 3.596 r_scbond_other 3.596 r_mcbond_it 3.226 r_mcbond_other 3.225 r_angle_refined_deg 1.661 r_angle_other_deg 0.995 r_chiral_restr 0.095 r_bond_refined_d 0.015 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 19202 Nucleic Acid Atoms Solvent Atoms 1130 Heterogen Atoms 173
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing