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yCP beta5-A49T-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 = 135.32 α = 90 b = 300.9 β = 112.81 c = 144.92 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 2012-05-13 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 2.5 30 98.9 0.052 16.4 366982 362946 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 2.5 2.6 92.3 0.421 3.9
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 2.51 15 362946 344798 18148 99.57 0.198 0.19458 0.1933 0.1982 0.2189 0.2246 RANDOM 62.692
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] 4.65 -1.74 -5.89 1.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.447 r_sphericity_free 27.536 r_sphericity_bonded 16.48 r_dihedral_angle_3_deg 14.411 r_dihedral_angle_4_deg 14.342 r_dihedral_angle_1_deg 5.173 r_long_range_B_refined 3.239 r_long_range_B_other 3.225 r_mcangle_it 2.873 r_mcangle_other 2.873
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.447 r_sphericity_free 27.536 r_sphericity_bonded 16.48 r_dihedral_angle_3_deg 14.411 r_dihedral_angle_4_deg 14.342 r_dihedral_angle_1_deg 5.173 r_long_range_B_refined 3.239 r_long_range_B_other 3.225 r_mcangle_it 2.873 r_mcangle_other 2.873 r_scangle_other 2.589 r_mcbond_it 2.175 r_mcbond_other 2.175 r_scbond_it 2.123 r_scbond_other 2.123 r_rigid_bond_restr 1.84 r_angle_refined_deg 0.899 r_angle_other_deg 0.705 r_chiral_restr 0.05 r_bond_refined_d 0.004 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 49370 Nucleic Acid Atoms Solvent Atoms 426 Heterogen Atoms 181
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing