5JUG

Structure of an inactive (E45Q) variant of a beta-1,4-mannanase, SsGH134, in complex with Man5


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otheralpha-helical fragment

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 NaHEPES, pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.3247

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.707α = 90
b = 53.841β = 90
c = 82.636γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-04-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.97949DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
10.9645.1184.10.0540.99812.45.984396
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)
10.960.9829.20.521.12.5

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 fragment0.9645.1180165416683.790.12270.121730.14133RANDOM9.503
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]
-0.13-0.120.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.746
r_sphericity_free26.134
r_dihedral_angle_4_deg15.197
r_dihedral_angle_3_deg10.388
r_sphericity_bonded6.962
r_dihedral_angle_1_deg4.993
r_long_range_B_refined2.969
r_long_range_B_other2.967
r_rigid_bond_restr1.798
r_scangle_other1.762
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.746
r_sphericity_free26.134
r_dihedral_angle_4_deg15.197
r_dihedral_angle_3_deg10.388
r_sphericity_bonded6.962
r_dihedral_angle_1_deg4.993
r_long_range_B_refined2.969
r_long_range_B_other2.967
r_rigid_bond_restr1.798
r_scangle_other1.762
r_angle_refined_deg1.668
r_mcangle_it1.371
r_mcangle_other1.371
r_scbond_it1.352
r_scbond_other1.349
r_angle_other_deg1.008
r_mcbond_other1.006
r_mcbond_it1.005
r_chiral_restr0.108
r_bond_refined_d0.012
r_gen_planes_refined0.01
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 Atoms1236
Nucleic Acid Atoms
Solvent Atoms228
Heterogen Atoms75

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
ACORNphasing