4B1L

CARBOHYDRATE BINDING MODULE CBM66 FROM BACILLUS SUBTILIS


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4AZZPDB ENTRY 4AZZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
125% (W/V) PEG 1500, 100MM MMT BUFFER, 5-6 MM LEVAN BIOSE.
Crystal Properties
Matthews coefficientSolvent content
1.727.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.616α = 90
b = 38.616β = 90
c = 162.391γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU R-AXIS IVMIRRORS2011-11-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007

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
11.6540.698.70.0718.78.9176592
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)
11.651.7491.30.493.15

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4AZZ1.6554.131669989998.580.179980.17610.25591RANDOM17.258
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]
-0.07-0.03-0.070.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.614
r_dihedral_angle_4_deg21.754
r_sphericity_free15.496
r_dihedral_angle_3_deg13.806
r_sphericity_bonded12.626
r_dihedral_angle_1_deg8.026
r_rigid_bond_restr3.432
r_angle_refined_deg1.456
r_chiral_restr0.104
r_bond_refined_d0.012
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.614
r_dihedral_angle_4_deg21.754
r_sphericity_free15.496
r_dihedral_angle_3_deg13.806
r_sphericity_bonded12.626
r_dihedral_angle_1_deg8.026
r_rigid_bond_restr3.432
r_angle_refined_deg1.456
r_chiral_restr0.104
r_bond_refined_d0.012
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_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1260
Nucleic Acid Atoms
Solvent Atoms56
Heterogen Atoms13

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing