2JD9

Structure of a pectin binding carbohydrate binding module determined in an orthorhombic crystal form.


X-RAY DIFFRACTION

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.0639.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.765α = 90
b = 42.63β = 90
c = 98.681γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODE

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
11.82096.20.0820.314129782
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)
11.81.8653.50.356.813.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.8201297868096.20.1750.1720.24RANDOM19.42
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]
-0.150.71-0.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg20.474
r_scangle_it4.791
r_scbond_it3.098
r_angle_refined_deg1.875
r_mcangle_it1.871
r_mcbond_it1.034
r_angle_other_deg0.963
r_symmetry_vdw_other0.303
r_nbd_other0.264
r_xyhbond_nbd_refined0.244
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg20.474
r_scangle_it4.791
r_scbond_it3.098
r_angle_refined_deg1.875
r_mcangle_it1.871
r_mcbond_it1.034
r_angle_other_deg0.963
r_symmetry_vdw_other0.303
r_nbd_other0.264
r_xyhbond_nbd_refined0.244
r_nbd_refined0.198
r_symmetry_hbond_refined0.195
r_chiral_restr0.128
r_nbtor_other0.098
r_symmetry_vdw_refined0.025
r_bond_refined_d0.021
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
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 Atoms1072
Nucleic Acid Atoms
Solvent Atoms196
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPphasing