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yCP beta5-C63F 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 = 138.14 α = 90 b = 299.96 β = 113.18 c = 146.57 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 2.9 30 98.6 0.077 13.9 241692 238309 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 0.51 3.1
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 238309 226393 11916 98.7 0.188 0.18483 0.18311 0.1917 0.21738 0.2244 RANDOM 72.881
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] 5.26 -0.73 -8.34 2.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.961 r_sphericity_free 29.821 r_sphericity_bonded 20.151 r_dihedral_angle_3_deg 13.948 r_dihedral_angle_4_deg 13.238 r_dihedral_angle_1_deg 4.977 r_long_range_B_refined 4.902 r_long_range_B_other 4.899 r_mcangle_it 4.284 r_mcangle_other 4.284
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.961 r_sphericity_free 29.821 r_sphericity_bonded 20.151 r_dihedral_angle_3_deg 13.948 r_dihedral_angle_4_deg 13.238 r_dihedral_angle_1_deg 4.977 r_long_range_B_refined 4.902 r_long_range_B_other 4.899 r_mcangle_it 4.284 r_mcangle_other 4.284 r_scangle_other 3.862 r_mcbond_it 3.198 r_mcbond_other 3.197 r_scbond_it 3.05 r_scbond_other 3.05 r_rigid_bond_restr 1.656 r_angle_refined_deg 0.848 r_angle_other_deg 0.693 r_chiral_restr 0.049 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 49376 Nucleic Acid Atoms Solvent Atoms 253 Heterogen Atoms 177
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing