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yCP beta5-A49V 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 = 136.98 α = 90 b = 301.07 β = 112.89 c = 145.94 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 2012-09-22 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 98.5 0.077 10.4 332931 327937 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 99.1 0.429 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1RYP 2.6 15 327936 311539 16397 98.63 0.22 0.21749 0.21613 0.24322 0.2402 RANDOM 55.914
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] 2.01 -0.17 -4.04 1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.993 r_sphericity_free 29.329 r_dihedral_angle_3_deg 14.339 r_sphericity_bonded 14.046 r_dihedral_angle_4_deg 13.5 r_dihedral_angle_1_deg 5.018 r_long_range_B_refined 3.601 r_long_range_B_other 3.567 r_mcangle_it 3.098 r_mcangle_other 3.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.993 r_sphericity_free 29.329 r_dihedral_angle_3_deg 14.339 r_sphericity_bonded 14.046 r_dihedral_angle_4_deg 13.5 r_dihedral_angle_1_deg 5.018 r_long_range_B_refined 3.601 r_long_range_B_other 3.567 r_mcangle_it 3.098 r_mcangle_other 3.098 r_scangle_other 2.711 r_mcbond_it 2.333 r_mcbond_other 2.333 r_scbond_it 2.183 r_scbond_other 2.183 r_rigid_bond_restr 1.499 r_angle_refined_deg 0.897 r_angle_other_deg 0.788 r_chiral_restr 0.052 r_bond_refined_d 0.005 r_bond_other_d 0.003 r_gen_planes_refined 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 49300 Nucleic Acid Atoms Solvent Atoms 704 Heterogen Atoms 346
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing