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yCP in complex with tripeptidic epoxyketone inhibitor 9
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, 100mM MES, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.67 66.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.88 α = 90 b = 299.38 β = 112.78 c = 144.83 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 93.1 0.11 7.3 2.7 259355 241410 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 97.5 0.487 2.1
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 241410 229339 12071 93.2 0.229 0.22408 0.22281 0.2251 0.24805 0.2485 RANDOM 54.596
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] 2.42 0.07 -3.8 1
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 38.697 r_dihedral_angle_2_deg 36.608 r_dihedral_angle_3_deg 17.875 r_dihedral_angle_4_deg 16.22 r_sphericity_bonded 7.845 r_dihedral_angle_1_deg 6.132 r_long_range_B_refined 3.339 r_long_range_B_other 3.326 r_mcangle_it 2.873 r_mcangle_other 2.873
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 38.697 r_dihedral_angle_2_deg 36.608 r_dihedral_angle_3_deg 17.875 r_dihedral_angle_4_deg 16.22 r_sphericity_bonded 7.845 r_dihedral_angle_1_deg 6.132 r_long_range_B_refined 3.339 r_long_range_B_other 3.326 r_mcangle_it 2.873 r_mcangle_other 2.873 r_scangle_other 2.643 r_mcbond_it 2.266 r_mcbond_other 2.265 r_scbond_it 2.262 r_scbond_other 2.262 r_rigid_bond_restr 1.8 r_angle_refined_deg 1.013 r_angle_other_deg 0.724 r_chiral_restr 0.057 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 49296 Nucleic Acid Atoms Solvent Atoms 245 Heterogen Atoms 124
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing