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yCP beta5-M45T mutant in complex with bortezomib
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 = 136.1 α = 90 b = 300.82 β = 113.06 c = 144.82 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 2013-08-14 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 2.3 30 98.9 0.055 13.7 472659 467460 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 2.3 2.4 99.4 0.52 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 2.3 15 467460 444087 23373 98.99 0.209 0.20668 0.2057 0.2114 0.22542 0.2311 RANDOM 58.986
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] 2.23 -0.83 -4.89 2.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.721 r_sphericity_free 25.135 r_sphericity_bonded 16.642 r_dihedral_angle_3_deg 13.514 r_dihedral_angle_4_deg 12.751 r_dihedral_angle_1_deg 4.991 r_long_range_B_refined 2.823 r_long_range_B_other 2.715 r_mcangle_it 2.286 r_mcangle_other 2.286
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.721 r_sphericity_free 25.135 r_sphericity_bonded 16.642 r_dihedral_angle_3_deg 13.514 r_dihedral_angle_4_deg 12.751 r_dihedral_angle_1_deg 4.991 r_long_range_B_refined 2.823 r_long_range_B_other 2.715 r_mcangle_it 2.286 r_mcangle_other 2.286 r_scangle_other 1.969 r_mcbond_other 1.774 r_mcbond_it 1.773 r_scbond_it 1.662 r_scbond_other 1.662 r_rigid_bond_restr 0.91 r_angle_refined_deg 0.836 r_angle_other_deg 0.69 r_chiral_restr 0.048 r_bond_refined_d 0.004 r_bond_other_d 0.002 r_gen_planes_refined 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 49364 Nucleic Acid Atoms Solvent Atoms 1604 Heterogen Atoms 181
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing