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yCP in complex with tripeptidic epoxyketone inhibitor 8
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, 100mM MES, 13% MPD, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.74 67.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.65 α = 90 b = 299.59 β = 112.85 c = 144.82 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 2.4 20 98.3 0.052 13.6 3.1 416796 409646 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 2.4 2.5 99.1 0.443 2.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1RYP 2.4 15 2 409646 389163 20483 98.39 0.201 0.19946 0.19866 0.21482 0.2097 RANDOM 59.86
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] 2.61 -0.32 -6.78 3.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.371 r_sphericity_free 27.344 r_dihedral_angle_4_deg 19.223 r_dihedral_angle_3_deg 18.15 r_dihedral_angle_1_deg 6.346 r_sphericity_bonded 4.78 r_long_range_B_refined 2.607 r_long_range_B_other 2.55 r_scbond_it 2.193 r_scbond_other 2.193
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.371 r_sphericity_free 27.344 r_dihedral_angle_4_deg 19.223 r_dihedral_angle_3_deg 18.15 r_dihedral_angle_1_deg 6.346 r_sphericity_bonded 4.78 r_long_range_B_refined 2.607 r_long_range_B_other 2.55 r_scbond_it 2.193 r_scbond_other 2.193 r_mcangle_it 2.169 r_mcangle_other 2.169 r_scangle_other 2.116 r_mcbond_it 1.925 r_mcbond_other 1.925 r_rigid_bond_restr 1.136 r_angle_refined_deg 1.119 r_angle_other_deg 0.797 r_chiral_restr 0.063 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 812 Heterogen Atoms 224
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing