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yCP in complex with tripeptidic epoxyketone inhibitor 11
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 20mM MGAC2, 13% MPD, PH 6.8, 100mM MES, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.67 66.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.42 α = 90 b = 299.95 β = 113.18 c = 145.96 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 2013-10-26 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 2.8 20 96.2 0.078 11.7 3 264104 254162 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 2.8 2.9 97.1 0.491 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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-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 2.8 15 2 254162 241453 12709 96.36 0.183 0.17997 0.17899 0.1809 0.19857 0.1961 RANDOM 61.06
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] 2.1 -0.1 -6.36 3.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.863 r_sphericity_free 30.719 r_dihedral_angle_4_deg 18.907 r_dihedral_angle_3_deg 18.464 r_dihedral_angle_1_deg 6.613 r_sphericity_bonded 5.401 r_long_range_B_refined 2.984 r_long_range_B_other 2.973 r_mcangle_it 2.643 r_mcangle_other 2.643
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.863 r_sphericity_free 30.719 r_dihedral_angle_4_deg 18.907 r_dihedral_angle_3_deg 18.464 r_dihedral_angle_1_deg 6.613 r_sphericity_bonded 5.401 r_long_range_B_refined 2.984 r_long_range_B_other 2.973 r_mcangle_it 2.643 r_mcangle_other 2.643 r_scangle_other 2.544 r_scbond_it 2.505 r_scbond_other 2.505 r_mcbond_it 2.245 r_mcbond_other 2.245 r_rigid_bond_restr 2.207 r_angle_refined_deg 1.099 r_angle_other_deg 0.763 r_chiral_restr 0.062 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 189 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing