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Crystal Structure of levansucrase from Gluconacetobacter diazotrophicus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OYG PDB ENTRY 1OYG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 0.5M AS, 30% ETHANOL, 0.1M NA-CITRATE PH5.6, pH 5.60
Crystal Properties Matthews coefficient Solvent content 3 58.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.803 α = 90 b = 119.391 β = 90 c = 215.101 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC CCD 2001-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 2.5 51.98 99.2 0.08 6.9 3.3 48568 2
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 2.5 2.64 98.5 0.32 2 3.2
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1OYG 2.5 105.41 46069 2444 99 0.2 0.197 0.2103 0.25 RANDOM 24.33
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] -2.06 4.57 -2.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.555 r_dihedral_angle_4_deg 22.644 r_dihedral_angle_3_deg 18.132 r_dihedral_angle_1_deg 7.656 r_scangle_it 1.92 r_angle_refined_deg 1.509 r_scbond_it 1.232 r_angle_other_deg 0.886 r_mcangle_it 0.786 r_mcbond_it 0.612
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.555 r_dihedral_angle_4_deg 22.644 r_dihedral_angle_3_deg 18.132 r_dihedral_angle_1_deg 7.656 r_scangle_it 1.92 r_angle_refined_deg 1.509 r_scbond_it 1.232 r_angle_other_deg 0.886 r_mcangle_it 0.786 r_mcbond_it 0.612 r_symmetry_hbond_refined 0.28 r_symmetry_vdw_other 0.219 r_nbd_refined 0.209 r_nbd_other 0.2 r_xyhbond_nbd_refined 0.175 r_symmetry_vdw_refined 0.143 r_nbtor_other 0.09 r_chiral_restr 0.089 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7635 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing