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Crystal structure of B. subtilis levansucrase mutant D247A
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 2.01 38.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.158 α = 90 b = 67.351 β = 90 c = 123.792 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 2003-03-07 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 99.5 0.038 0.038 25 8.7 26627 26627
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 99 0.068 0.068 25.1 8.1
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 25579 25579 1290 99.56 0.171 0.171 0.169 0.1836 0.215 0.2177 RANDOM 12.073
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] -0.43 0.04 0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.813 r_scangle_it 1.745 r_angle_refined_deg 1.193 r_scbond_it 1.133 r_angle_other_deg 0.773 r_mcangle_it 0.621 r_mcbond_it 0.34 r_symmetry_hbond_refined 0.285 r_symmetry_vdw_other 0.28 r_nbd_other 0.238
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.813 r_scangle_it 1.745 r_angle_refined_deg 1.193 r_scbond_it 1.133 r_angle_other_deg 0.773 r_mcangle_it 0.621 r_mcbond_it 0.34 r_symmetry_hbond_refined 0.285 r_symmetry_vdw_other 0.28 r_nbd_other 0.238 r_nbd_refined 0.193 r_symmetry_vdw_refined 0.141 r_xyhbond_nbd_refined 0.125 r_nbtor_other 0.08 r_chiral_restr 0.078 r_metal_ion_refined 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3439 Nucleic Acid Atoms Solvent Atoms 271 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling