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Levansucrase from Brenneria sp. EniD 312 at 1.33 angstroms resolution
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 7.5 298.15 Ammonium sulfate, PEG 400
Crystal Properties Matthews coefficient Solvent content 3.14 60.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98 α = 90 b = 98 β = 90 c = 213.539 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 2017-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97853 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 1.33 84.87 90.3 0.019 0.999 20.1 36.8 138038
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.33 1.4 34.5 0.012 0.706 16.1
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-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 1.33 84.8 138038 96.8 0.164 0.1452 0.176 0.1699 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.561 r_dihedral_angle_4_deg 22.96 r_dihedral_angle_3_deg 12.235 r_dihedral_angle_1_deg 6.754 r_long_range_B_refined 3.454 r_long_range_B_other 3.013 r_rigid_bond_restr 2.676 r_scangle_other 2.618 r_scbond_it 2.193 r_scbond_other 2.189
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.561 r_dihedral_angle_4_deg 22.96 r_dihedral_angle_3_deg 12.235 r_dihedral_angle_1_deg 6.754 r_long_range_B_refined 3.454 r_long_range_B_other 3.013 r_rigid_bond_restr 2.676 r_scangle_other 2.618 r_scbond_it 2.193 r_scbond_other 2.189 r_mcangle_it 1.863 r_mcangle_other 1.863 r_angle_refined_deg 1.685 r_mcbond_it 1.452 r_mcbond_other 1.421 r_angle_other_deg 1.171 r_chiral_restr 0.114 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3276 Nucleic Acid Atoms Solvent Atoms 491 Heterogen Atoms 144
Software Software Software Name Purpose REFMAC refinement xia2 data scaling PDB_EXTRACT data extraction xia2 data reduction PHASER phasing