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yCP in complex with tripeptidic epoxyketone inhibitor 17
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 = 136.04 α = 90 b = 300.38 β = 112.97 c = 146.52 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 2.9 20 95.4 0.085 8.5 2.6 238743 227749 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 97.4 0.451 1.9
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 2.9 15 2 227749 216361 11388 95.51 0.189 0.18511 0.18385 0.1846 0.20947 0.2072 RANDOM 73.807
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] 5.26 1.88 -11.42 3.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.089 r_sphericity_free 31.464 r_dihedral_angle_3_deg 19.528 r_dihedral_angle_4_deg 17.552 r_sphericity_bonded 7.564 r_dihedral_angle_1_deg 6.462 r_long_range_B_refined 4.181 r_long_range_B_other 4.168 r_mcangle_it 3.788 r_mcangle_other 3.788
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.089 r_sphericity_free 31.464 r_dihedral_angle_3_deg 19.528 r_dihedral_angle_4_deg 17.552 r_sphericity_bonded 7.564 r_dihedral_angle_1_deg 6.462 r_long_range_B_refined 4.181 r_long_range_B_other 4.168 r_mcangle_it 3.788 r_mcangle_other 3.788 r_scangle_other 3.504 r_scbond_it 3.189 r_scbond_other 3.189 r_mcbond_it 3.114 r_mcbond_other 3.114 r_rigid_bond_restr 1.793 r_angle_refined_deg 1.121 r_angle_other_deg 0.778 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 49295 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 116
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing