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Crystal structure of Leuconostoc citreum NRRL B-1299 N-terminally truncated dextransucrase DSR-M
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AIB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 PEG 3350 20%, 0.1M BIS-TRIS pH 6.5, 0.4M KSCN
Crystal Properties Matthews coefficient Solvent content 3.05 59.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.84 α = 90 b = 128.71 β = 90 c = 229.34 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 PIXEL DECTRIS PILATUS3 2M 2015-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 3.2 114.67 98.7 0.15 8.8 5.2 51658
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 3.2 3.37 98.4 0.453 1.7 4.2
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3AIB 3.2 114.67 49085 2531 98.4 0.2226 0.2213 0.2223 0.2482 0.2481 RANDOM 53.518
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] -2.36 -2.1 4.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.763 r_dihedral_angle_4_deg 16.526 r_dihedral_angle_3_deg 15.28 r_dihedral_angle_1_deg 6.388 r_mcangle_it 1.411 r_angle_refined_deg 1.207 r_angle_other_deg 1.084 r_mcbond_it 0.854 r_mcbond_other 0.853 r_chiral_restr 0.068
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.763 r_dihedral_angle_4_deg 16.526 r_dihedral_angle_3_deg 15.28 r_dihedral_angle_1_deg 6.388 r_mcangle_it 1.411 r_angle_refined_deg 1.207 r_angle_other_deg 1.084 r_mcbond_it 0.854 r_mcbond_other 0.853 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18003 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 14
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction PHASER phasing