5WAG

ADC-7 in complex with boronic acid transition state inhibitor S06017


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4U0T 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5298ADC-7 (3mg/mL) in 25% w/v polyethylene glycol (PEG) 1500, 0.1 M succinate/ phosphate/ glycine
Crystal Properties
Matthews coefficientSolvent content
2.1242.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.665α = 90
b = 80.896β = 113.36
c = 105.338γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2013-08-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.07821APS21-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.93181.39797.40.0780.99810.83.899952
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9311.93895.90.6320.7092.13.9

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 REPLACEMENTTHROUGHOUT4U0T1.93181.39794942498797.330.189140.186080.24714RANDOM35.98
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]
0.420.97-1.2-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.12
r_dihedral_angle_4_deg22.277
r_dihedral_angle_3_deg15.275
r_dihedral_angle_1_deg6.997
r_long_range_B_refined6.07
r_long_range_B_other6.066
r_scangle_other5.02
r_mcangle_it3.841
r_mcangle_other3.841
r_scbond_it3.496
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.12
r_dihedral_angle_4_deg22.277
r_dihedral_angle_3_deg15.275
r_dihedral_angle_1_deg6.997
r_long_range_B_refined6.07
r_long_range_B_other6.066
r_scangle_other5.02
r_mcangle_it3.841
r_mcangle_other3.841
r_scbond_it3.496
r_scbond_other3.496
r_mcbond_it2.908
r_mcbond_other2.907
r_angle_refined_deg1.864
r_angle_other_deg1.112
r_chiral_restr0.111
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms11033
Nucleic Acid Atoms
Solvent Atoms389
Heterogen Atoms72

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building