4CD4

The structure of GH26 beta-mannanase CjMan26C from Cellvibrio japonicus in complex with ManIFG


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VX7PDB ENTRY 2VX7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.6100 MM SODIUM CITRATE PH 5.6, 15% PEG 3000
Crystal Properties
Matthews coefficientSolvent content
2.856

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.518α = 90
b = 84.518β = 90
c = 244.491γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMIRRORS2013-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I02DiamondI02

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
11.254.4688.80.0621.914.81421502
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)
11.21.2220.80.690.81.4

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2VX71.273.19134854714588.730.112410.111290.13385RANDOM15.02
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]
0.030.010.03-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free34.159
r_dihedral_angle_2_deg33.127
r_dihedral_angle_4_deg15.114
r_dihedral_angle_3_deg11.237
r_sphericity_bonded8.371
r_dihedral_angle_1_deg5.88
r_rigid_bond_restr2.391
r_scangle_it1.768
r_angle_refined_deg1.519
r_scbond_it1.51
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free34.159
r_dihedral_angle_2_deg33.127
r_dihedral_angle_4_deg15.114
r_dihedral_angle_3_deg11.237
r_sphericity_bonded8.371
r_dihedral_angle_1_deg5.88
r_rigid_bond_restr2.391
r_scangle_it1.768
r_angle_refined_deg1.519
r_scbond_it1.51
r_angle_other_deg1.285
r_mcangle_it1.228
r_mcbond_it0.99
r_mcbond_other0.989
r_symmetry_vdw_refined0.379
r_nbd_refined0.272
r_symmetry_vdw_other0.247
r_nbd_other0.196
r_nbtor_refined0.187
r_xyhbond_nbd_refined0.138
r_metal_ion_refined0.126
r_chiral_restr0.099
r_symmetry_hbond_refined0.083
r_nbtor_other0.079
r_xyhbond_nbd_other0.014
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_gen_planes_other0.003
r_bond_other_d0.001
r_metal_ion_other
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 Atoms2933
Nucleic Acid Atoms
Solvent Atoms746
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing