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yCP beta5-A49T-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 = 136.71 α = 90 b = 300.14 β = 113.16 c = 145.28 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 2.9 30 98.5 0.075 12.9 237365 233805 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 99.4 0.538 2.9
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 2.9 15 233804 222113 11691 98.65 0.196 0.19285 0.191 0.1965 0.22824 0.2317 RANDOM 67.548
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] 2.89 -0.34 -6 2.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.308 r_sphericity_free 33.553 r_sphericity_bonded 18.02 r_dihedral_angle_3_deg 14.655 r_dihedral_angle_4_deg 13.842 r_dihedral_angle_1_deg 5.155 r_long_range_B_refined 4.625 r_long_range_B_other 4.614 r_mcangle_it 4.175 r_mcangle_other 4.175
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.308 r_sphericity_free 33.553 r_sphericity_bonded 18.02 r_dihedral_angle_3_deg 14.655 r_dihedral_angle_4_deg 13.842 r_dihedral_angle_1_deg 5.155 r_long_range_B_refined 4.625 r_long_range_B_other 4.614 r_mcangle_it 4.175 r_mcangle_other 4.175 r_scangle_other 3.687 r_mcbond_it 3.138 r_mcbond_other 3.138 r_scbond_it 2.919 r_scbond_other 2.919 r_rigid_bond_restr 1.232 r_angle_refined_deg 0.912 r_angle_other_deg 0.795 r_chiral_restr 0.051 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 49235 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 347
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing