5BV9

The Structure of Bacillus pumilus GH48 in complex with cellobiose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1G9GPDB entry 1G9G

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP52932.4 M Sodium malonate, pH 5.0
Crystal Properties
Matthews coefficientSolvent content
3.2361.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.291α = 90
b = 97.291β = 90
c = 218.108γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 1352011-02-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.935099.80.17139.588.7279431
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.932.0399.92.033.93

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 1G9G1.935074971395099.310.16360.161320.20747RANDOM17.43
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]
0.580.58-1.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.338
r_dihedral_angle_4_deg16.353
r_dihedral_angle_3_deg14.05
r_dihedral_angle_1_deg6.799
r_long_range_B_refined6.75
r_long_range_B_other5.721
r_scangle_other3.728
r_scbond_it2.404
r_scbond_other2.403
r_mcangle_other2.278
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.338
r_dihedral_angle_4_deg16.353
r_dihedral_angle_3_deg14.05
r_dihedral_angle_1_deg6.799
r_long_range_B_refined6.75
r_long_range_B_other5.721
r_scangle_other3.728
r_scbond_it2.404
r_scbond_other2.403
r_mcangle_other2.278
r_mcangle_it2.276
r_angle_refined_deg1.912
r_mcbond_it1.534
r_mcbond_other1.512
r_angle_other_deg1.108
r_chiral_restr0.126
r_bond_refined_d0.02
r_gen_planes_refined0.011
r_bond_other_d0.003
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5581
Nucleic Acid Atoms
Solvent Atoms950
Heterogen Atoms94

Software

Software
Software NamePurpose
REFMACrefinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
MOLREPphasing