4QLS

yCP in complex with tripeptidic epoxyketone inhibitor 11


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RYP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.829320mM MGAC2, 13% MPD, PH 6.8, 100mM MES, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.6766.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.42α = 90
b = 299.95β = 113.18
c = 145.96γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2013-10-26MSINGLE 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
12.82096.20.07811.7326410425416222
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)
12.82.997.10.4912.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)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 REPLACEMENTTHROUGHOUT1RYP2.81522541622414531270996.360.1830.179970.178990.19857RANDOM61.06
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]
2.1-0.1-6.363.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.863
r_sphericity_free30.719
r_dihedral_angle_4_deg18.907
r_dihedral_angle_3_deg18.464
r_dihedral_angle_1_deg6.613
r_sphericity_bonded5.401
r_long_range_B_refined2.984
r_long_range_B_other2.973
r_mcangle_it2.643
r_mcangle_other2.643
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.863
r_sphericity_free30.719
r_dihedral_angle_4_deg18.907
r_dihedral_angle_3_deg18.464
r_dihedral_angle_1_deg6.613
r_sphericity_bonded5.401
r_long_range_B_refined2.984
r_long_range_B_other2.973
r_mcangle_it2.643
r_mcangle_other2.643
r_scangle_other2.544
r_scbond_it2.505
r_scbond_other2.505
r_mcbond_it2.245
r_mcbond_other2.245
r_rigid_bond_restr2.207
r_angle_refined_deg1.099
r_angle_other_deg0.763
r_chiral_restr0.062
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 Atoms49296
Nucleic Acid Atoms
Solvent Atoms189
Heterogen Atoms116

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing