2WHJ

Understanding how diverse mannanases recognise heterogeneous substrates


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BQCPDB ENTRY 1BQC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
11.8M AMSO4, 0.1M NA-CITRATE PH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.5251

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.97α = 90
b = 111.97β = 90
c = 47.4γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODE

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
11.7820940.05424.4328782
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)
11.781.84450.16.81.8

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 1BQC1.7895.3529323158093.90.1220.1190.173RANDOM15.82
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]
0.640.320.64-0.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.388
r_dihedral_angle_3_deg11.692
r_dihedral_angle_4_deg10.808
r_dihedral_angle_1_deg7.499
r_sphericity_free6.652
r_scangle_it4.095
r_sphericity_bonded3.571
r_scbond_it2.834
r_mcangle_it1.89
r_rigid_bond_restr1.824
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.388
r_dihedral_angle_3_deg11.692
r_dihedral_angle_4_deg10.808
r_dihedral_angle_1_deg7.499
r_sphericity_free6.652
r_scangle_it4.095
r_sphericity_bonded3.571
r_scbond_it2.834
r_mcangle_it1.89
r_rigid_bond_restr1.824
r_angle_refined_deg1.5
r_mcbond_it1.236
r_nbtor_refined0.31
r_symmetry_vdw_refined0.283
r_symmetry_hbond_refined0.242
r_nbd_refined0.201
r_xyhbond_nbd_refined0.131
r_chiral_restr0.12
r_bond_refined_d0.018
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_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 Atoms2417
Nucleic Acid Atoms
Solvent Atoms380
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing