4QZ1

yCP beta5-M45T 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 = 137.18α = 90
b = 298.8β = 113.02
c = 146.83γ = 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 X06SASLSX06SA

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
133097.90.0977.821680321225022
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)
133.199.10.4682.1

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 1RYP3152122492016361061398.050.177970.175990.21573RANDOM84.253
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]
6.39-2.28-8.542.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.933
r_sphericity_free31.79
r_sphericity_bonded24.508
r_dihedral_angle_3_deg14.001
r_dihedral_angle_4_deg13.684
r_long_range_B_refined6.165
r_long_range_B_other6.159
r_mcangle_it5.481
r_mcangle_other5.481
r_dihedral_angle_1_deg4.986
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.933
r_sphericity_free31.79
r_sphericity_bonded24.508
r_dihedral_angle_3_deg14.001
r_dihedral_angle_4_deg13.684
r_long_range_B_refined6.165
r_long_range_B_other6.159
r_mcangle_it5.481
r_mcangle_other5.481
r_dihedral_angle_1_deg4.986
r_scangle_other4.957
r_mcbond_it4.063
r_mcbond_other4.062
r_scbond_it3.886
r_scbond_other3.885
r_rigid_bond_restr1.374
r_angle_refined_deg0.898
r_angle_other_deg0.857
r_chiral_restr0.05
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 Atoms49276
Nucleic Acid Atoms
Solvent Atoms217
Heterogen Atoms305

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing