4YZX

C. bescii Family 3 pectate lyase double mutant K108A/D107N in complex with trigalacturonic acid


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82930.1 M Tris pH 8 and 61% MPD
Crystal Properties
Matthews coefficientSolvent content
2.0941.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 138.334α = 90
b = 36.352β = 132.67
c = 100.106γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-03-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.983970SSRLBL11-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.2534.5895.115.56.891778
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.251.2793.11.9

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 DIFFRACTIONTHROUGHOUT1.2534.5891778459294.70.1120.110.156RANDOM17.05
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]
0.260.33-0.83-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.77
r_dihedral_angle_4_deg30.627
r_sphericity_free20.819
r_sphericity_bonded14.649
r_dihedral_angle_3_deg12.05
r_dihedral_angle_1_deg6.712
r_rigid_bond_restr6.665
r_long_range_B_refined5.051
r_scangle_other4.798
r_scbond_it4.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.77
r_dihedral_angle_4_deg30.627
r_sphericity_free20.819
r_sphericity_bonded14.649
r_dihedral_angle_3_deg12.05
r_dihedral_angle_1_deg6.712
r_rigid_bond_restr6.665
r_long_range_B_refined5.051
r_scangle_other4.798
r_scbond_it4.58
r_scbond_other4.58
r_long_range_B_other4.531
r_mcangle_it2.407
r_mcangle_other2.407
r_mcbond_other2.152
r_mcbond_it2.151
r_angle_refined_deg2.043
r_angle_other_deg0.927
r_chiral_restr0.125
r_bond_refined_d0.02
r_gen_planes_refined0.011
r_gen_planes_other0.003
r_bond_other_d0.002
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2973
Nucleic Acid Atoms
Solvent Atoms578
Heterogen Atoms179

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing