4D3L

SeMet structure of a novel carbohydrate binding module from glycoside hydrolase family 9 (Cel9A) from Ruminococcus flavefaciens FD-1 in the orthorhombic form


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
170.2 M SODIUM CITRATE, 2 M AMMONIUM SULPHATE. CRYOPROTECTANT USED PARATONE N, pH 7.0
Crystal Properties
Matthews coefficientSolvent content
3.1961

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.302α = 90
b = 103.345β = 90
c = 109.067γ = 90
Symmetry
Space GroupI 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-07-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 1SOLEILPROXIMA 1

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
1243.631000.165.25.737050
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)
122.1169.90.690.92.2

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 DIFFRACTIONSADTHROUGHOUTNONE275.0235182184893.620.213620.212010.24523RANDOM35.825
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]
-0.10.81-0.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.992
r_dihedral_angle_4_deg26.194
r_dihedral_angle_3_deg13.868
r_dihedral_angle_1_deg6.454
r_mcangle_it2.751
r_scbond_it2.643
r_mcbond_other1.857
r_mcbond_it1.856
r_angle_refined_deg1.414
r_angle_other_deg1.037
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.992
r_dihedral_angle_4_deg26.194
r_dihedral_angle_3_deg13.868
r_dihedral_angle_1_deg6.454
r_mcangle_it2.751
r_scbond_it2.643
r_mcbond_other1.857
r_mcbond_it1.856
r_angle_refined_deg1.414
r_angle_other_deg1.037
r_chiral_restr0.081
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.005
r_gen_planes_other0.005
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 Atoms3054
Nucleic Acid Atoms
Solvent Atoms235
Heterogen Atoms77

Software

Software
Software NamePurpose
PARROTmodel building
Aimlessdata scaling
SHELXphasing
CCP4phasing
PHASERphasing
PARROTphasing
REFMACrefinement