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Crystal structure of B. subtilis levansucrase mutant D86A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OYG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICRODIALYSIS 6.3 291 diammonium phosphate, sodium acetate, pH 6.3, MICRODIALYSIS, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2 38.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.075 α = 90 b = 67.132 β = 90 c = 123.676 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 IMAGE PLATE MAC Science DIP-2030B 2003-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.07 30 90.8 0.039 0.039 24.7 3.4 24114 24114
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.07 2.14 88.1 0.067 0.067 25 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1OYG 2.1 30 23261 23261 1179 91.07 0.165 0.165 0.162 0.1746 0.208 0.2187 RANDOM 12.285
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] -0.22 0.19 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.815 r_scangle_it 1.715 r_angle_refined_deg 1.197 r_scbond_it 1.117 r_angle_other_deg 0.78 r_mcangle_it 0.613 r_mcbond_it 0.344 r_symmetry_vdw_other 0.291 r_symmetry_hbond_refined 0.286 r_nbd_other 0.239
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.815 r_scangle_it 1.715 r_angle_refined_deg 1.197 r_scbond_it 1.117 r_angle_other_deg 0.78 r_mcangle_it 0.613 r_mcbond_it 0.344 r_symmetry_vdw_other 0.291 r_symmetry_hbond_refined 0.286 r_nbd_other 0.239 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.153 r_xyhbond_nbd_refined 0.139 r_metal_ion_refined 0.138 r_nbtor_other 0.081 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3439 Nucleic Acid Atoms Solvent Atoms 265 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling