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yCP in complex with Z-Leu-Leu-Leu-epoxyketone
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, 100 mM MES, 13% MPD, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.71 66.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.49 α = 90 b = 301.49 β = 114.15 c = 144.39 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 2011-07-09 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 2.6 25 99.3 0.09 8.84 3 397998 395212 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 2.6 2.7 99.6 0.503 1.99
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 11599 98.95 0.185 0.17876 0.17747 0.1812 0.20342 0.2054 RANDOM 57.381
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] 2.88 -1.16 -8.05 4.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.323 r_sphericity_free 34.329 r_dihedral_angle_3_deg 17.676 r_dihedral_angle_4_deg 16.935 r_sphericity_bonded 7.85 r_dihedral_angle_1_deg 6.026 r_angle_refined_deg 1.013 r_rigid_bond_restr 0.878 r_angle_other_deg 0.724 r_chiral_restr 0.058
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.323 r_sphericity_free 34.329 r_dihedral_angle_3_deg 17.676 r_dihedral_angle_4_deg 16.935 r_sphericity_bonded 7.85 r_dihedral_angle_1_deg 6.026 r_angle_refined_deg 1.013 r_rigid_bond_restr 0.878 r_angle_other_deg 0.724 r_chiral_restr 0.058 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 49294 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 160
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing