4QZ1

yCP beta5-M45T mutant in complex with the epoxyketone inhibitor ONX 0914


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.8
Temperature 293.0
Details 20 MM MGAC2, 13% MPD, PH 6.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 137.18 α = 90
b = 298.8 β = 113.02
c = 146.83 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PSI PILATUS 6M -- 2013-08-14
Diffraction Radiation
Monochromator Protocol
LN2 COOLED FIXED-EXIT. SI(111) MONOCHROMATOR SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06SA -- SLS X06SA

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
3 30 97.9 0.097 -- -- -- 216803 212250 2.0 2.0 --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
3.0 3.1 99.1 0.468 -- 2.1 -- --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 3.0 15.0 -- -- 212249 201636 10613 98.05 -- 0.17797 0.17599 0.21573 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 3.0 3.075 -- 764 14507 0.271 0.325 -- 99.19
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 84.253
Anisotropic B[1][1] 6.39
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -2.28
Anisotropic B[2][2] -8.54
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.29
RMS Deviations
Key Refinement Restraint Deviation
r_rigid_bond_restr 1.374
r_mcangle_it 5.481
r_mcangle_other 5.481
r_scangle_other 4.957
r_bond_refined_d 0.005
r_dihedral_angle_1_deg 4.986
r_scbond_it 3.886
r_scbond_other 3.885
r_gen_planes_refined 0.003
r_angle_other_deg 0.857
r_dihedral_angle_3_deg 14.001
r_chiral_restr 0.05
r_mcbond_it 4.063
r_mcbond_other 4.062
r_bond_other_d 0.002
r_dihedral_angle_4_deg 13.684
r_long_range_B_refined 6.165
r_dihedral_angle_2_deg 33.933
r_long_range_B_other 6.159
r_sphericity_free 31.79
r_sphericity_bonded 24.508
r_angle_refined_deg 0.898
r_gen_planes_other 0.001
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 49276
Nucleic Acid Atoms 0
Heterogen Atoms 305
Solvent Atoms 217

Software

Software
Software Name Purpose
XDS data scaling
REFMAC refinement
XDS data reduction
XSCALE data scaling
REFMAC phasing