6ZBM

Structure of the D125N mutant of the catalytic domain of the Bacillus circulans alpha-1,6 Mannanase in complex with an alpha-1,6-alpha-manno-cyclophellitol carbasugar-stabilised trisaccharide inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4D4A4D4A.PDB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP291PEG 3350, ammonium nitrate
Crystal Properties
Matthews coefficientSolvent content
1.7228.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.768α = 90
b = 66.121β = 100.23
c = 49.397γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-01-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)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
11.4766.1299.80.130.953.1447092
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.471.599.70.6310.6761.13.4

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 REPLACEMENTTHROUGHOUT4D4A.PDB1.4748.6644764230499.810.16160.15860.218RANDOM13.884
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]
0.431.30.31-1.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.858
r_dihedral_angle_4_deg23.188
r_dihedral_angle_3_deg13.359
r_dihedral_angle_1_deg6.156
r_rigid_bond_restr4.62
r_angle_refined_deg1.722
r_angle_other_deg1.632
r_chiral_restr0.093
r_bond_refined_d0.012
r_gen_planes_refined0.011
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.858
r_dihedral_angle_4_deg23.188
r_dihedral_angle_3_deg13.359
r_dihedral_angle_1_deg6.156
r_rigid_bond_restr4.62
r_angle_refined_deg1.722
r_angle_other_deg1.632
r_chiral_restr0.093
r_bond_refined_d0.012
r_gen_planes_refined0.011
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2625
Nucleic Acid Atoms
Solvent Atoms178
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing