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Levansucrase from Brenneria sp. EniD 312
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4D47
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 Ammonium sulfate, PEG 400
Crystal Properties Matthews coefficient Solvent content 3.25 62.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.314 α = 90 b = 98.314 β = 90 c = 216.475 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 XE 16M 2020-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.34 85.15 94.6 0.025 17.4 39 80004
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.34 1.39 82.3 0.456
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 4D47 1.6 85.14 69526 3686 89.16 0.1584 0.1572 0.1693 0.1809 0.1889 RANDOM 18.853
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] 0.09 0.05 0.09 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.552 r_dihedral_angle_4_deg 22.708 r_dihedral_angle_3_deg 13.078 r_dihedral_angle_1_deg 7.398 r_angle_refined_deg 1.725 r_angle_other_deg 1.443 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.552 r_dihedral_angle_4_deg 22.708 r_dihedral_angle_3_deg 13.078 r_dihedral_angle_1_deg 7.398 r_angle_refined_deg 1.725 r_angle_other_deg 1.443 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3281 Nucleic Acid Atoms Solvent Atoms 564 Heterogen Atoms 149
Software Software Software Name Purpose REFMAC refinement xia2 data scaling PDB_EXTRACT data extraction xia2 data reduction PHASER phasing