2WHL

Understanding how diverse mannanases recognise heterogeneous substrates


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WHJPDB ENTRY 2WHJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
11.6M NA/K PO4, 0.1M HEPES PH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.2846.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.255α = 90
b = 63.69β = 90
c = 83.577γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
11.419.73950.05273.7623702
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)
11.41.45680.23.52.3

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 2WHJ1.450.6455790298094.20.1520.150.188RANDOM16.22
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]
4.52-2.32-2.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.176
r_sphericity_free12.157
r_dihedral_angle_3_deg11.34
r_dihedral_angle_4_deg10.432
r_sphericity_bonded7.546
r_dihedral_angle_1_deg6.722
r_scangle_it5.783
r_scbond_it4.289
r_mcangle_it2.939
r_rigid_bond_restr2.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.176
r_sphericity_free12.157
r_dihedral_angle_3_deg11.34
r_dihedral_angle_4_deg10.432
r_sphericity_bonded7.546
r_dihedral_angle_1_deg6.722
r_scangle_it5.783
r_scbond_it4.289
r_mcangle_it2.939
r_rigid_bond_restr2.36
r_mcbond_it2.167
r_angle_refined_deg1.96
r_angle_other_deg1.618
r_mcbond_other1.261
r_chiral_restr0.304
r_bond_refined_d0.021
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.001
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2312
Nucleic Acid Atoms
Solvent Atoms273
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing