4QZX

yCP beta5-C63F mutant in complex with the epoxyketone inhibitor ONX 0914


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RYP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.829320 MM MGAC2, 13% MPD, PH 6.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties
Matthews coefficientSolvent content
3.6766.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 137.21α = 90
b = 300.81β = 113.52
c = 145.09γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2013-08-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0SLSX06SA

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
12.63098.20.06610.832983132389422
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)
12.62.799.40.4552.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1RYP2.6153238933076981619598.360.2010.198810.197540.22293RANDOM67.386
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]
2.78-1.88-6.193.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.166
r_sphericity_free27.56
r_sphericity_bonded19.496
r_dihedral_angle_4_deg14.128
r_dihedral_angle_3_deg14.084
r_dihedral_angle_1_deg5.07
r_long_range_B_refined3.918
r_long_range_B_other3.901
r_mcangle_it3.505
r_mcangle_other3.505
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.166
r_sphericity_free27.56
r_sphericity_bonded19.496
r_dihedral_angle_4_deg14.128
r_dihedral_angle_3_deg14.084
r_dihedral_angle_1_deg5.07
r_long_range_B_refined3.918
r_long_range_B_other3.901
r_mcangle_it3.505
r_mcangle_other3.505
r_scangle_other3.012
r_mcbond_it2.614
r_mcbond_other2.614
r_scbond_it2.409
r_scbond_other2.409
r_rigid_bond_restr1.171
r_angle_refined_deg0.893
r_angle_other_deg0.807
r_chiral_restr0.051
r_bond_refined_d0.005
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms49279
Nucleic Acid Atoms
Solvent Atoms455
Heterogen Atoms310

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing