2WDA

The X-ray structure of the Streptomyces coelicolor A3 Chondroitin AC Lyase in Complex with Chondroitin sulphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WCOPDB ENTRY 2WCO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14 M NA FORMATE,20 % GLYCEROL AS CRYOPROTECTANT
Crystal Properties
Matthews coefficientSolvent content
359

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 140.508α = 90
b = 140.508β = 90
c = 100.764γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2005-05-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-3ESRFID14-3

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
12.350.31000.097.68.1453612
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)
12.32.41000.3958.2

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2WCO2.349.684301122881000.1510.1490.193RANDOM25.08
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]
0.010.01-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.103
r_dihedral_angle_4_deg17.97
r_dihedral_angle_3_deg13.966
r_dihedral_angle_1_deg6.454
r_scangle_it5.084
r_scbond_it3.42
r_angle_refined_deg1.953
r_mcangle_it1.822
r_mcbond_it1.034
r_chiral_restr0.132
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.103
r_dihedral_angle_4_deg17.97
r_dihedral_angle_3_deg13.966
r_dihedral_angle_1_deg6.454
r_scangle_it5.084
r_scbond_it3.42
r_angle_refined_deg1.953
r_mcangle_it1.822
r_mcbond_it1.034
r_chiral_restr0.132
r_bond_refined_d0.023
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_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 Atoms5667
Nucleic Acid Atoms
Solvent Atoms499
Heterogen Atoms127

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing