4QZ0

yCP beta5-M45V 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 = 136.05α = 90
b = 299.92β = 112.94
c = 145.01γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2013-09-07MSINGLE 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
133097.70.0812.721324620834122
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)
133.198.90.423.2

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 REPLACEMENTTHROUGHOUT1RYP3152083411979241041797.850.1730.170410.168790.20146RANDOM73.904
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]
3.84-0.95-7.763.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.817
r_sphericity_free26.854
r_sphericity_bonded23.476
r_dihedral_angle_3_deg13.733
r_dihedral_angle_4_deg13.362
r_dihedral_angle_1_deg4.985
r_long_range_B_refined4.633
r_long_range_B_other4.632
r_mcangle_it4.089
r_mcangle_other4.089
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.817
r_sphericity_free26.854
r_sphericity_bonded23.476
r_dihedral_angle_3_deg13.733
r_dihedral_angle_4_deg13.362
r_dihedral_angle_1_deg4.985
r_long_range_B_refined4.633
r_long_range_B_other4.632
r_mcangle_it4.089
r_mcangle_other4.089
r_scangle_other3.717
r_mcbond_it3.026
r_mcbond_other3.026
r_scbond_it2.923
r_scbond_other2.923
r_rigid_bond_restr1.267
r_angle_refined_deg0.885
r_angle_other_deg0.821
r_chiral_restr0.05
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 Atoms49294
Nucleic Acid Atoms
Solvent Atoms141
Heterogen Atoms308

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing