4QLV

yCP in complex with tripeptidic epoxyketone inhibitor 17


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, 100mM MES, 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 = 136.04α = 90
b = 300.38β = 112.97
c = 146.52γ = 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
12.92095.40.0858.52.623874322774922
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)
12.9397.40.4511.9

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 REPLACEMENTTHROUGHOUT1RYP2.91522277492163611138895.510.1890.185110.183850.20947RANDOM73.807
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]
5.261.88-11.423.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.089
r_sphericity_free31.464
r_dihedral_angle_3_deg19.528
r_dihedral_angle_4_deg17.552
r_sphericity_bonded7.564
r_dihedral_angle_1_deg6.462
r_long_range_B_refined4.181
r_long_range_B_other4.168
r_mcangle_it3.788
r_mcangle_other3.788
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.089
r_sphericity_free31.464
r_dihedral_angle_3_deg19.528
r_dihedral_angle_4_deg17.552
r_sphericity_bonded7.564
r_dihedral_angle_1_deg6.462
r_long_range_B_refined4.181
r_long_range_B_other4.168
r_mcangle_it3.788
r_mcangle_other3.788
r_scangle_other3.504
r_scbond_it3.189
r_scbond_other3.189
r_mcbond_it3.114
r_mcbond_other3.114
r_rigid_bond_restr1.793
r_angle_refined_deg1.121
r_angle_other_deg0.778
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 Atoms49295
Nucleic Acid Atoms
Solvent Atoms211
Heterogen Atoms116

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing