4CD5

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.6100MM SODIUM CITRATE PH 5.6, 15% PEG 3000
Crystal Properties
Matthews coefficientSolvent content
2.8156

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.507α = 90
b = 84.507β = 90
c = 244.941γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMIRRORS2012-07-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I03DiamondI03

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
11.1321000.111.715.32085892
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.11.12100110

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 2VX71.173.191978441055599.980.152730.151710.17213RANDOM14.118
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]
-0.36-0.18-0.361.17
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free37.761
r_dihedral_angle_2_deg33.231
r_rigid_bond_restr19.642
r_dihedral_angle_4_deg15.365
r_sphericity_bonded12.176
r_dihedral_angle_3_deg11.447
r_dihedral_angle_1_deg5.919
r_scangle_it3.207
r_scbond_it2.657
r_mcangle_it2.217
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free37.761
r_dihedral_angle_2_deg33.231
r_rigid_bond_restr19.642
r_dihedral_angle_4_deg15.365
r_sphericity_bonded12.176
r_dihedral_angle_3_deg11.447
r_dihedral_angle_1_deg5.919
r_scangle_it3.207
r_scbond_it2.657
r_mcangle_it2.217
r_mcbond_other1.918
r_mcbond_it1.917
r_angle_refined_deg1.549
r_angle_other_deg0.916
r_nbd_refined0.259
r_symmetry_vdw_refined0.254
r_symmetry_vdw_other0.203
r_nbtor_refined0.185
r_nbd_other0.176
r_xyhbond_nbd_refined0.127
r_metal_ion_refined0.107
r_chiral_restr0.103
r_symmetry_hbond_refined0.082
r_nbtor_other0.08
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_gen_planes_other0.003
r_bond_other_d0.001
r_xyhbond_nbd_other
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 Atoms2935
Nucleic Acid Atoms
Solvent Atoms494
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing