4QW1

yCP beta5-A50V mutant in complex with bortezomib


X-RAY DIFFRACTION

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 = 135.35α = 90
b = 299.86β = 112.95
c = 144.82γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2012-10-20MSINGLE 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
12.93096.20.08610.423439722549022
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)
12.9397.80.4952.9

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 REPLACEMENTTHROUGHOUT1RYP2.9152254902142151127596.330.1910.188180.18670.21636RANDOM60.888
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]
3.42-1.46-4.941.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.139
r_sphericity_free28.57
r_sphericity_bonded17.648
r_dihedral_angle_3_deg13.878
r_dihedral_angle_4_deg13.396
r_dihedral_angle_1_deg5.065
r_long_range_B_refined3.782
r_long_range_B_other3.772
r_mcangle_it3.225
r_mcangle_other3.225
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.139
r_sphericity_free28.57
r_sphericity_bonded17.648
r_dihedral_angle_3_deg13.878
r_dihedral_angle_4_deg13.396
r_dihedral_angle_1_deg5.065
r_long_range_B_refined3.782
r_long_range_B_other3.772
r_mcangle_it3.225
r_mcangle_other3.225
r_scangle_other2.996
r_mcbond_it2.424
r_mcbond_other2.424
r_scbond_it2.399
r_scbond_other2.399
r_rigid_bond_restr1.34
r_angle_refined_deg0.844
r_angle_other_deg0.682
r_chiral_restr0.048
r_bond_refined_d0.004
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms49370
Nucleic Acid Atoms
Solvent Atoms335
Heterogen Atoms181

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing