5JU9

Structure of a beta-1,4-mannanase, SsGH134, in complex with Man3.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7293The protein stock in the buffer of 20 mM sodium phosphate, pH7.2, and 200 mM NaCl is mixed 1:1 with the precipitant consist of 20% PEG6000, 0.15-0.2 M CaCl2, and 0.1 M Na HEPES, pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.346.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.68α = 90
b = 53.63β = 90
c = 82.14γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.97949DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.1844.9197.516.6752763
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)
11.181.2180.20.5582.43.7

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 REPLACEMENTTHROUGHOUTalpha-helical fragment1.1844.9150049264797.390.13250.131430.15313RANDOM13.909
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]
0.090.11-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.944
r_sphericity_free28.502
r_dihedral_angle_4_deg23.61
r_dihedral_angle_3_deg11.877
r_sphericity_bonded7.764
r_dihedral_angle_1_deg5.096
r_long_range_B_refined2.689
r_long_range_B_other2.688
r_scangle_other2.158
r_scbond_it1.702
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.944
r_sphericity_free28.502
r_dihedral_angle_4_deg23.61
r_dihedral_angle_3_deg11.877
r_sphericity_bonded7.764
r_dihedral_angle_1_deg5.096
r_long_range_B_refined2.689
r_long_range_B_other2.688
r_scangle_other2.158
r_scbond_it1.702
r_scbond_other1.701
r_mcangle_it1.604
r_mcangle_other1.603
r_angle_refined_deg1.574
r_rigid_bond_restr1.492
r_mcbond_it1.247
r_mcbond_other1.247
r_angle_other_deg1.062
r_chiral_restr0.107
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1230
Nucleic Acid Atoms
Solvent Atoms162
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
ACORNphasing