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Crystal structure of dextranase from Streptococcus mutans in complex with isomaltotriose
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 293 30% PEGMME 2000, 0.1M phosphate-citrate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.2 44.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.031 α = 90 b = 90.34 β = 100.33 c = 63.001 γ = 90
Symmetry Space Group P 1 21 1
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 RIGAKU RAXIS VII 2006-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.9 50 99.7 0.057 46.1 9.6 49514 40.7
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 1.9 1.97 100 0.408 8.4 9.4 4954
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 1.9 29.22 46979 2507 99.56 0.18952 0.18696 0.1858 0.2366 0.2342 RANDOM 35.115
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] 0.03 -0.01 -0.03 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.256 r_dihedral_angle_4_deg 15.746 r_dihedral_angle_3_deg 14.548 r_dihedral_angle_1_deg 6.448 r_scangle_it 4.118 r_scbond_it 2.632 r_mcangle_it 1.772 r_angle_refined_deg 1.57 r_mcbond_it 1.006 r_chiral_restr 0.111
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.256 r_dihedral_angle_4_deg 15.746 r_dihedral_angle_3_deg 14.548 r_dihedral_angle_1_deg 6.448 r_scangle_it 4.118 r_scbond_it 2.632 r_mcangle_it 1.772 r_angle_refined_deg 1.57 r_mcbond_it 1.006 r_chiral_restr 0.111 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 4985 Nucleic Acid Atoms Solvent Atoms 275 Heterogen Atoms 73
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling