5VMA

Structure of B. pumilus GH48 in complex with a cellobio-derived isofagomine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4EL8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP294screen containing 2-3 M sodium malonate pH 5-7
Crystal Properties
Matthews coefficientSolvent content
3.3262.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.891α = 90
b = 98.891β = 90
c = 216.799γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 1352013-01-03MSINGLE 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
11.955099.40.100816.559.978718
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.952.0595.60.48122.663.9

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 REPLACEMENTTHROUGHOUT4EL81.955073422379697.60.1560.1540.196RANDOM18.09
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]
0.730.73-1.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.668
r_dihedral_angle_4_deg14.688
r_dihedral_angle_3_deg13.3
r_dihedral_angle_1_deg6.871
r_long_range_B_refined5.216
r_long_range_B_other5.08
r_scangle_other3.919
r_scbond_it2.606
r_scbond_other2.606
r_mcangle_other2.491
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.668
r_dihedral_angle_4_deg14.688
r_dihedral_angle_3_deg13.3
r_dihedral_angle_1_deg6.871
r_long_range_B_refined5.216
r_long_range_B_other5.08
r_scangle_other3.919
r_scbond_it2.606
r_scbond_other2.606
r_mcangle_other2.491
r_mcangle_it2.49
r_angle_refined_deg1.968
r_mcbond_it1.699
r_mcbond_other1.694
r_angle_other_deg1.204
r_chiral_restr0.139
r_bond_refined_d0.021
r_gen_planes_refined0.012
r_bond_other_d0.004
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 Atoms5552
Nucleic Acid Atoms
Solvent Atoms579
Heterogen Atoms147

Software

Software
Software NamePurpose
REFMACrefinement
PROTEUM PLUSdata collection
PROTEUM PLUSdata processing
MOLREPphasing