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yCP beta5-A49S-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 = 136.15 α = 90 b = 300.26 β = 113 c = 145.44 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 99 0.07 11.9 328459 325174 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 99.5 0.463 2.7
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 325174 308915 16259 99.08 0.196 0.19274 0.19164 0.1963 0.21371 0.2183 RANDOM 63.089
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 -0.44 -5.87 2.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.27 r_sphericity_free 25.128 r_sphericity_bonded 16.128 r_dihedral_angle_3_deg 14.472 r_dihedral_angle_4_deg 14.099 r_dihedral_angle_1_deg 5.102 r_long_range_B_refined 3.196 r_long_range_B_other 3.189 r_mcangle_it 2.87 r_mcangle_other 2.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.27 r_sphericity_free 25.128 r_sphericity_bonded 16.128 r_dihedral_angle_3_deg 14.472 r_dihedral_angle_4_deg 14.099 r_dihedral_angle_1_deg 5.102 r_long_range_B_refined 3.196 r_long_range_B_other 3.189 r_mcangle_it 2.87 r_mcangle_other 2.87 r_scangle_other 2.588 r_mcbond_it 2.177 r_mcbond_other 2.177 r_scbond_it 2.114 r_scbond_other 2.114 r_rigid_bond_restr 0.907 r_angle_refined_deg 0.878 r_angle_other_deg 0.773 r_chiral_restr 0.05 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 49297 Nucleic Acid Atoms Solvent Atoms 219 Heterogen Atoms 347
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing