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Crystal structure of B. subtilis levansucrase mutant E342A bound to raffinose
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 38.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.211 α = 90 b = 66.7 β = 90 c = 124.042 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-2030 2003-03-05 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 2.03 62.02 98.2 0.053 0.053 25.1 5 27688 27688
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 2.03 2.1 98.1 0.097 0.097 25.5 4.5
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 25079 23811 1268 98.23 0.185 0.18144 0.17923 0.1822 0.22357 0.2258 RANDOM 15.237
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] -0.52 0.93 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.685 r_dihedral_angle_4_deg 14.683 r_dihedral_angle_3_deg 11.329 r_dihedral_angle_1_deg 5.963 r_scangle_it 1.144 r_angle_refined_deg 1.066 r_scbond_it 0.715 r_mcangle_it 0.416 r_nbtor_refined 0.299 r_mcbond_it 0.248
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.685 r_dihedral_angle_4_deg 14.683 r_dihedral_angle_3_deg 11.329 r_dihedral_angle_1_deg 5.963 r_scangle_it 1.144 r_angle_refined_deg 1.066 r_scbond_it 0.715 r_mcangle_it 0.416 r_nbtor_refined 0.299 r_mcbond_it 0.248 r_symmetry_vdw_refined 0.188 r_nbd_refined 0.179 r_symmetry_hbond_refined 0.124 r_xyhbond_nbd_refined 0.11 r_metal_ion_refined 0.087 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3438 Nucleic Acid Atoms Solvent Atoms 275 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling