5ZYB

Crystal structure of MOX-1 complexed with a boronic acid transition state inhibitor S02030


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3W8K 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5289PEG 8000, 100 mM sodium cacodylate buffer (pH 6.5), 0.2 M zinc acetate
Crystal Properties
Matthews coefficientSolvent content
2.2344.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.64α = 90
b = 59.2β = 102.03
c = 62.89γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2016-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0Photon FactoryBL-5A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.1361.5199.910.83.220024
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.132.18100

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 REPLACEMENTTHROUGHOUT3W8K2.1342.691905095799.840.159790.157530.2048RANDOM23.931
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]
0.111.41-1.851.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.804
r_dihedral_angle_4_deg17.721
r_dihedral_angle_3_deg12.629
r_dihedral_angle_1_deg6.768
r_long_range_B_refined5.149
r_long_range_B_other5.119
r_scangle_other3.683
r_scbond_it2.355
r_scbond_other2.355
r_mcangle_it2.276
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.804
r_dihedral_angle_4_deg17.721
r_dihedral_angle_3_deg12.629
r_dihedral_angle_1_deg6.768
r_long_range_B_refined5.149
r_long_range_B_other5.119
r_scangle_other3.683
r_scbond_it2.355
r_scbond_other2.355
r_mcangle_it2.276
r_mcangle_other2.275
r_mcbond_it1.533
r_mcbond_other1.511
r_angle_refined_deg1.279
r_angle_other_deg0.95
r_chiral_restr0.063
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.001
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 Atoms2631
Nucleic Acid Atoms
Solvent Atoms186
Heterogen Atoms65

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing