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Crystal structure of dextranase from Streptococcus mutans in complex with 4,5-epoxypentyl alpha-D-glucopyranoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VMN
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 39.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.428 α = 90 b = 89.966 β = 102.25 c = 62.842 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 315 2008-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 1.88 61.41 98.3 0.085 28.9 6.9 45454 29.4
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 89.7 0.267 5.4 5.6 4112
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 3VMN 1.88 50 43068 2306 96.66 0.19762 0.19548 0.195 0.23771 0.2367 RANDOM 26.537
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] 3.57 0.42 -0.93 -2.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.232 r_dihedral_angle_4_deg 17.295 r_dihedral_angle_3_deg 13.298 r_dihedral_angle_1_deg 6.809 r_scangle_it 4.029 r_scbond_it 2.519 r_mcangle_it 1.591 r_angle_refined_deg 1.538 r_mcbond_it 0.907 r_chiral_restr 0.114
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.232 r_dihedral_angle_4_deg 17.295 r_dihedral_angle_3_deg 13.298 r_dihedral_angle_1_deg 6.809 r_scangle_it 4.029 r_scbond_it 2.519 r_mcangle_it 1.591 r_angle_refined_deg 1.538 r_mcbond_it 0.907 r_chiral_restr 0.114 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 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 5012 Nucleic Acid Atoms Solvent Atoms 373 Heterogen Atoms 23
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling