4V17

Structure of a novel carbohydrate binding module from glycoside hydrolase family 5 glucanase from Ruminococcus flavefaciens FD-1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherSEMET DERIVATIVE FROM 2.28 A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.51.2 M NA2 CITRATE, 0.1 M HEPES PH 7.5 CRYO 30% GLYCEROL IN ABOVE CONDITION
Crystal Properties
Matthews coefficientSolvent content
2.5752

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.093α = 90
b = 131.093β = 90
c = 105.199γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-05-06MSINGLE 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
1230.171000.1212.516.926385
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)
122.051001.51.715.2

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 REPLACEMENTTHROUGHOUTSEMET DERIVATIVE FROM 2.28 A277.1622333120099.760.204030.202690.22875RANDOM57.336
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]
0.950.480.95-3.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.534
r_dihedral_angle_3_deg14.216
r_dihedral_angle_1_deg6.849
r_mcangle_it4.084
r_scbond_it3.705
r_mcbond_it2.662
r_mcbond_other2.662
r_angle_refined_deg1.263
r_angle_other_deg0.868
r_chiral_restr0.073
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.534
r_dihedral_angle_3_deg14.216
r_dihedral_angle_1_deg6.849
r_mcangle_it4.084
r_scbond_it3.705
r_mcbond_it2.662
r_mcbond_other2.662
r_angle_refined_deg1.263
r_angle_other_deg0.868
r_chiral_restr0.073
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.003
r_dihedral_angle_4_deg
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2289
Nucleic Acid Atoms
Solvent Atoms85
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing