7NL5

Structure of the catalytic domain of the Bacillus circulans alpha-1,6 Mannanase in complex with an alpha-1,6-alpha-manno-cyclophellitol trisaccharide inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4D4A 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP291PEG 3350, ammonium nitrate pH 6.5
Crystal Properties
Matthews coefficientSolvent content
1.6827

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.521α = 90
b = 65.415β = 101.9
c = 49.442γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-02-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97950DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.465.4199.40.9936.43.853069
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.420.742

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 REPLACEMENTTHROUGHOUT4D4A1.448.4350450257699.250.14830.14710.1733RANDOM16.589
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]
0.780.880.1-1.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.525
r_dihedral_angle_4_deg22.427
r_dihedral_angle_3_deg12.043
r_dihedral_angle_1_deg5.799
r_angle_refined_deg1.831
r_angle_other_deg1.691
r_chiral_restr0.099
r_bond_refined_d0.012
r_gen_planes_refined0.011
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.525
r_dihedral_angle_4_deg22.427
r_dihedral_angle_3_deg12.043
r_dihedral_angle_1_deg5.799
r_angle_refined_deg1.831
r_angle_other_deg1.691
r_chiral_restr0.099
r_bond_refined_d0.012
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2658
Nucleic Acid Atoms
Solvent Atoms295
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
Aimlessdata scaling
REFMACphasing