4QZ3

yCP beta5-A49V mutant in complex with the epoxyketone inhibitor ONX 0914


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RYPpdb entry 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 = 135.76α = 90
b = 300.17β = 112.96
c = 144.96γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2012-05-13MSINGLE 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
12.83097.20.0849.225432022
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)
12.82.998.80.4822.3

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1RYP2.8152543192416031271697.320.181880.180540.20748RANDOM64.466
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]
2.64-0.16-6.232.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.342
r_sphericity_free28.619
r_sphericity_bonded16.203
r_dihedral_angle_3_deg14.733
r_dihedral_angle_4_deg14.482
r_dihedral_angle_1_deg5.141
r_long_range_B_refined3.596
r_long_range_B_other3.584
r_mcangle_it3.159
r_mcangle_other3.159
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.342
r_sphericity_free28.619
r_sphericity_bonded16.203
r_dihedral_angle_3_deg14.733
r_dihedral_angle_4_deg14.482
r_dihedral_angle_1_deg5.141
r_long_range_B_refined3.596
r_long_range_B_other3.584
r_mcangle_it3.159
r_mcangle_other3.159
r_scangle_other2.884
r_mcbond_it2.364
r_mcbond_other2.364
r_scbond_it2.315
r_scbond_other2.315
r_rigid_bond_restr1.635
r_angle_refined_deg0.902
r_angle_other_deg0.813
r_chiral_restr0.052
r_bond_refined_d0.004
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 Atoms49300
Nucleic Acid Atoms
Solvent Atoms332
Heterogen Atoms285

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing