4QLQ

yCP in complex with tripeptidic epoxyketone inhibitor 8


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, 100mM MES, 13% MPD, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.7467.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.65α = 90
b = 299.59β = 112.85
c = 144.82γ = 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
12.42098.30.05213.63.141679640964622
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)
12.42.599.10.4432.8

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 REPLACEMENTTHROUGHOUT1RYP2.41524096463891632048398.390.2010.199460.198660.21482RANDOM59.86
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]
2.61-0.32-6.783.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.371
r_sphericity_free27.344
r_dihedral_angle_4_deg19.223
r_dihedral_angle_3_deg18.15
r_dihedral_angle_1_deg6.346
r_sphericity_bonded4.78
r_long_range_B_refined2.607
r_long_range_B_other2.55
r_scbond_it2.193
r_scbond_other2.193
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.371
r_sphericity_free27.344
r_dihedral_angle_4_deg19.223
r_dihedral_angle_3_deg18.15
r_dihedral_angle_1_deg6.346
r_sphericity_bonded4.78
r_long_range_B_refined2.607
r_long_range_B_other2.55
r_scbond_it2.193
r_scbond_other2.193
r_mcangle_it2.169
r_mcangle_other2.169
r_scangle_other2.116
r_mcbond_it1.925
r_mcbond_other1.925
r_rigid_bond_restr1.136
r_angle_refined_deg1.119
r_angle_other_deg0.797
r_chiral_restr0.063
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 Atoms812
Heterogen Atoms224

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing