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Levansucrase from Brenneria sp. EniD 312 with sucrose
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 3.03 59.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.125 α = 90 b = 98.125 β = 90 c = 215.534 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 PILATUS3 6M 2020-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.9762 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.18 84.98 80.7 1 18.8 38.1 161790
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.18 1.2 5.9 0.644
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4D47 1.35 84.98 127550 6601 99.89 0.1301 0.1291 0.1498 0.1677 RANDOM 15.974
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] -0.83 -0.41 -0.83 2.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.882 r_dihedral_angle_4_deg 21.11 r_dihedral_angle_3_deg 11.511 r_dihedral_angle_1_deg 7.233 r_rigid_bond_restr 4.653 r_angle_refined_deg 1.545 r_angle_other_deg 1.392 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.882 r_dihedral_angle_4_deg 21.11 r_dihedral_angle_3_deg 11.511 r_dihedral_angle_1_deg 7.233 r_rigid_bond_restr 4.653 r_angle_refined_deg 1.545 r_angle_other_deg 1.392 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3276 Nucleic Acid Atoms Solvent Atoms 550 Heterogen Atoms 147
Software Software Software Name Purpose REFMAC refinement xia2 data scaling PDB_EXTRACT data extraction xia2 data reduction PHASER phasing