4QLT

yCP in complex with tripeptidic epoxyketone inhibitor 2 (PR924)


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, 100 mM MES, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.6766.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.65α = 90
b = 298.66β = 112.83
c = 145.46γ = 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
12.82094.70.08610.32.926127324744022
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)
12.82.996.70.5022.6

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 REPLACEMENTTHROUGHOUT1RYP2.81522474392350671237294.820.1830.177610.176320.2021RANDOM62.112
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]
3.20.15-7.182.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.256
r_dihedral_angle_4_deg18.598
r_dihedral_angle_3_deg17.84
r_dihedral_angle_1_deg6.056
r_mcangle_it2.821
r_mcangle_other2.821
r_scangle_other2.69
r_scbond_it2.333
r_scbond_other2.333
r_mcbond_it2.239
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.256
r_dihedral_angle_4_deg18.598
r_dihedral_angle_3_deg17.84
r_dihedral_angle_1_deg6.056
r_mcangle_it2.821
r_mcangle_other2.821
r_scangle_other2.69
r_scbond_it2.333
r_scbond_other2.333
r_mcbond_it2.239
r_mcbond_other2.239
r_angle_refined_deg1.004
r_angle_other_deg0.717
r_chiral_restr0.057
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 Atoms49296
Nucleic Acid Atoms
Solvent Atoms567
Heterogen Atoms124

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing