3VMN

Crystal structure of dextranase from Streptococcus mutans


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
2.0339.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.2α = 90
b = 89.735β = 102.32
c = 63.258γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 2702007-06-26MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A0.9700, 0.97888, 0.97931, 0.98400, 0.96400Photon FactoryBL-17A

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
11.661.781000.06339.27.57668313.5
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)
11.61.661000.17511.57.57641

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 DIFFRACTIONMADTHROUGHOUT1.65072799384699.540.152920.15140.18179RANDOM12.693
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.575
r_dihedral_angle_4_deg16.09
r_dihedral_angle_3_deg12.599
r_dihedral_angle_1_deg6.395
r_scangle_it4.921
r_scbond_it3.049
r_mcangle_it1.987
r_angle_refined_deg1.823
r_mcbond_it1.136
r_chiral_restr0.135
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.575
r_dihedral_angle_4_deg16.09
r_dihedral_angle_3_deg12.599
r_dihedral_angle_1_deg6.395
r_scangle_it4.921
r_scbond_it3.049
r_mcangle_it1.987
r_angle_refined_deg1.823
r_mcbond_it1.136
r_chiral_restr0.135
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_bond_other_d
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_sphericity_bonded
r_mcbond_other
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_rigid_bond_restr
r_sphericity_free
r_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5020
Nucleic Acid Atoms
Solvent Atoms587
Heterogen Atoms5

Software

Software
Software NamePurpose
ADSCdata collection
SOLVEphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling