5AWV

Crystal structure of glycopeptide hexose oxidase DBV29 complexed with teicoplanin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WDW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP529317% PEG 3350, 0.2M diammonium hydrogen citrate, pH 5.0
Crystal Properties
Matthews coefficientSolvent content
2.4249.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.791α = 90
b = 150.778β = 98.4
c = 124.853γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152013-03-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B11NSRRCBL13B1

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
11.9329.5197.80.09114.974.6163843
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)
11.931.9697.10.5732.874.6

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 REPLACEMENTTHROUGHOUT2WDW1.9329.4155630821497.580.158420.155940.20464RANDOM32.621
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]
-2.12-1.06-0.042.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.726
r_dihedral_angle_4_deg17.994
r_dihedral_angle_3_deg15.113
r_long_range_B_refined9.135
r_long_range_B_other9.135
r_dihedral_angle_1_deg6.761
r_scangle_other6.407
r_scbond_it4.245
r_scbond_other4.245
r_mcangle_it3.956
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.726
r_dihedral_angle_4_deg17.994
r_dihedral_angle_3_deg15.113
r_long_range_B_refined9.135
r_long_range_B_other9.135
r_dihedral_angle_1_deg6.761
r_scangle_other6.407
r_scbond_it4.245
r_scbond_other4.245
r_mcangle_it3.956
r_mcangle_other3.956
r_mcbond_it2.839
r_mcbond_other2.822
r_angle_refined_deg2.162
r_angle_other_deg1.252
r_chiral_restr0.134
r_bond_refined_d0.022
r_gen_planes_refined0.013
r_bond_other_d0.004
r_gen_planes_other0.003
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms16104
Nucleic Acid Atoms
Solvent Atoms1400
Heterogen Atoms615

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing