2Q1F

Crystal structure of chondroitin sulfate lyase abc from bacteroides thetaiotaomicron wal2926


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.528217% PEG 3350, 0.2M ammonium sulfate, 100 mM HEPES , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 282K, pH 6.50
Crystal Properties
Matthews coefficientSolvent content
3.4464.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 223.362α = 90
b = 223.362β = 90
c = 112.639γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDDOUBLE-CRYSTAL FIXED-EXIT SI- 111 MONOCHROMATOR (E/E~10-4) AND A PLANAR PALLADIUM-COATED SILICON MIRROR2006-05-26MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-IDAPS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.855094.70.0630.0514.63.171079
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.852.9256.70.40.3261.61.7

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 DIFFRACTIONSADTHROUGHOUT2.855067482359994.80.2220.220.262RANDOM59.33
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]
-1.88-0.94-1.882.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.854
r_dihedral_angle_3_deg17.472
r_dihedral_angle_4_deg15.287
r_dihedral_angle_1_deg5.167
r_scangle_it1.864
r_mcangle_it1.214
r_scbond_it1.195
r_angle_refined_deg1.007
r_mcbond_it0.826
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.854
r_dihedral_angle_3_deg17.472
r_dihedral_angle_4_deg15.287
r_dihedral_angle_1_deg5.167
r_scangle_it1.864
r_mcangle_it1.214
r_scbond_it1.195
r_angle_refined_deg1.007
r_mcbond_it0.826
r_nbtor_refined0.3
r_nbd_refined0.189
r_symmetry_vdw_refined0.179
r_symmetry_hbond_refined0.176
r_xyhbond_nbd_refined0.111
r_metal_ion_refined0.073
r_chiral_restr0.07
r_bond_refined_d0.006
r_gen_planes_refined0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15824
Nucleic Acid Atoms
Solvent Atoms67
Heterogen Atoms82

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SHARPphasing