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Crystal structure of dextranase from Streptococcus mutans
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 2.03 39.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.2 α = 90 b = 89.735 β = 102.32 c = 63.258 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 95 CCD ADSC QUANTUM 270 2007-06-26 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.9700, 0.97888, 0.97931, 0.98400, 0.96400 Photon Factory BL-17A
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 1.6 61.78 100 0.063 39.2 7.5 76683 13.5
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 1.6 1.66 100 0.175 11.5 7.5 7641
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.6 50 72799 3846 99.54 0.15292 0.1514 0.18179 0.1891 RANDOM 12.693
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] 0.81 -0.01 -0.37 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.575 r_dihedral_angle_4_deg 16.09 r_dihedral_angle_3_deg 12.599 r_dihedral_angle_1_deg 6.395 r_scangle_it 4.921 r_scbond_it 3.049 r_mcangle_it 1.987 r_angle_refined_deg 1.823 r_mcbond_it 1.136 r_chiral_restr 0.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.575 r_dihedral_angle_4_deg 16.09 r_dihedral_angle_3_deg 12.599 r_dihedral_angle_1_deg 6.395 r_scangle_it 4.921 r_scbond_it 3.049 r_mcangle_it 1.987 r_angle_refined_deg 1.823 r_mcbond_it 1.136 r_chiral_restr 0.135 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 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 5020 Nucleic Acid Atoms Solvent Atoms 587 Heterogen Atoms 5
Software Software Software Name Purpose ADSC data collection SOLVE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling