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yCP beta5-A50V mutant in complex with carfilzomib
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, 13% MPD, 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 = 134.48 α = 90 b = 300.28 β = 112.71 c = 143.96 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 2012-10-20 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 30 98.1 0.064 14.3 322028 315909 2 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2.6 15 315908 300112 15796 98.38 0.197 0.19388 0.19258 0.2003 0.21856 0.2237 RANDOM 61.356
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] 2.96 -2.11 -5.43 2.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.066 r_sphericity_free 27.691 r_sphericity_bonded 17.215 r_dihedral_angle_3_deg 14.096 r_dihedral_angle_4_deg 13.631 r_dihedral_angle_1_deg 5.128 r_long_range_B_refined 3.369 r_long_range_B_other 3.339 r_mcangle_it 2.914 r_mcangle_other 2.914
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.066 r_sphericity_free 27.691 r_sphericity_bonded 17.215 r_dihedral_angle_3_deg 14.096 r_dihedral_angle_4_deg 13.631 r_dihedral_angle_1_deg 5.128 r_long_range_B_refined 3.369 r_long_range_B_other 3.339 r_mcangle_it 2.914 r_mcangle_other 2.914 r_scangle_other 2.575 r_mcbond_it 2.188 r_mcbond_other 2.188 r_scbond_it 2.095 r_scbond_other 2.095 r_rigid_bond_restr 0.904 r_angle_refined_deg 0.877 r_angle_other_deg 0.767 r_chiral_restr 0.049 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 49299 Nucleic Acid Atoms Solvent Atoms 652 Heterogen Atoms 348
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing