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yCP in complex with the epoxyketone inhibitor ONX 0914
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RYP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 293 20 MM MGAC2, 13% MPD, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, pH 6.8
Crystal Properties Matthews coefficient Solvent content 3.67 66.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.6 α = 90 b = 300.05 β = 112.77 c = 145.62 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL PSI PILATUS 6M 2013-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1 2.9 30 95.8 0.087 9.8 236478 226546 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3 97.2 0.539 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1RYP 2.9 15 226546 215218 11328 95.87 0.177 0.17366 0.17166 0.1769 0.21169 0.2161 RANDOM 75.235
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] 2.43 0.07 -9 4.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.324 r_sphericity_free 34.147 r_sphericity_bonded 22.254 r_dihedral_angle_3_deg 14.416 r_dihedral_angle_4_deg 14.247 r_long_range_B_refined 5.361 r_long_range_B_other 5.358 r_dihedral_angle_1_deg 5.15 r_mcangle_it 4.64 r_mcangle_other 4.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.324 r_sphericity_free 34.147 r_sphericity_bonded 22.254 r_dihedral_angle_3_deg 14.416 r_dihedral_angle_4_deg 14.247 r_long_range_B_refined 5.361 r_long_range_B_other 5.358 r_dihedral_angle_1_deg 5.15 r_mcangle_it 4.64 r_mcangle_other 4.64 r_scangle_other 4.357 r_mcbond_it 3.433 r_mcbond_other 3.433 r_scbond_it 3.364 r_scbond_other 3.364 r_rigid_bond_restr 1.186 r_angle_refined_deg 0.892 r_angle_other_deg 0.802 r_chiral_restr 0.051 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 49296 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms 312
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing