2X09 | pdb_00002x09

Inhibition of the exo-beta-D-glucosaminidase CsxA by a glucosamine- configured castanospermine and an amino-australine analogue


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VZSPDB ENTRY 2VZS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.448.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.75α = 90
b = 121.95β = 90.65
c = 92.05γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray2912009-05-27MSINGLE 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
12.42097.50.145.52.6728912
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)
12.42.5394.90.323.32.5

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2VZS2.42072891365297.50.179340.176020.180.240320.24RANDOM16.64
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]
-0.21-0.390.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.992
r_dihedral_angle_4_deg18.028
r_dihedral_angle_3_deg15.618
r_dihedral_angle_1_deg6.557
r_scangle_it2.327
r_scbond_it1.497
r_angle_refined_deg1.352
r_mcangle_it0.891
r_mcbond_it0.482
r_chiral_restr0.089
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13024
Nucleic Acid Atoms
Solvent Atoms1441
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MERGEdata scaling
MOLREPphasing