4QZW

yCP beta5-C52F 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 = 136.66α = 90
b = 300.7β = 113.22
c = 145.38γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2013-11-30MSINGLE 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
133093.10.11411.721488520005822
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)
133.196.10.5593.4

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 REPLACEMENTTHROUGHOUT1RYP3152000581900551000393.230.189420.18790.21826RANDOM57.206
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]
3.12-0.34-5.812.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.102
r_sphericity_free29.292
r_sphericity_bonded17.022
r_dihedral_angle_3_deg14.342
r_dihedral_angle_4_deg13.962
r_dihedral_angle_1_deg5.082
r_long_range_B_refined3.685
r_long_range_B_other3.671
r_mcangle_it3.147
r_mcangle_other3.147
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.102
r_sphericity_free29.292
r_sphericity_bonded17.022
r_dihedral_angle_3_deg14.342
r_dihedral_angle_4_deg13.962
r_dihedral_angle_1_deg5.082
r_long_range_B_refined3.685
r_long_range_B_other3.671
r_mcangle_it3.147
r_mcangle_other3.147
r_scangle_other2.929
r_mcbond_it2.344
r_mcbond_other2.344
r_scbond_it2.309
r_scbond_other2.309
r_rigid_bond_restr1.06
r_angle_refined_deg0.881
r_angle_other_deg0.78
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 Atoms49306
Nucleic Acid Atoms
Solvent Atoms309
Heterogen Atoms202

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing