3VMO

Crystal structure of dextranase from Streptococcus mutans in complex with isomaltotriose


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.229330% PEGMME 2000, 0.1M phosphate-citrate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
2.244.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.031α = 90
b = 90.34β = 100.33
c = 63.001γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS VII2006-08-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.95099.70.05746.19.64951440.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.971000.4088.49.44954

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT1.929.2246979250799.560.189520.186960.2366RANDOM35.115
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.256
r_dihedral_angle_4_deg15.746
r_dihedral_angle_3_deg14.548
r_dihedral_angle_1_deg6.448
r_scangle_it4.118
r_scbond_it2.632
r_mcangle_it1.772
r_angle_refined_deg1.57
r_mcbond_it1.006
r_chiral_restr0.111
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.256
r_dihedral_angle_4_deg15.746
r_dihedral_angle_3_deg14.548
r_dihedral_angle_1_deg6.448
r_scangle_it4.118
r_scbond_it2.632
r_mcangle_it1.772
r_angle_refined_deg1.57
r_mcbond_it1.006
r_chiral_restr0.111
r_bond_refined_d0.018
r_gen_planes_refined0.008
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 AtomsNumber
Protein Atoms4985
Nucleic Acid Atoms
Solvent Atoms275
Heterogen Atoms73

Software

Software
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling