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yCP beta5-A49V 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 = 136.52 α = 90 b = 300.75 β = 113.24 c = 145.35 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 2.8 30 97.7 0.061 16.3 263779 257713 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 2.8 2.9 98.9 0.427 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 2.8 15 257713 244827 12886 97.83 0.204 0.20118 0.19939 0.2059 0.23547 0.2408 RANDOM 62.298
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] 3.42 -1.23 -5.6 1.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.122 r_sphericity_free 29.549 r_sphericity_bonded 17.44 r_dihedral_angle_3_deg 14.05 r_dihedral_angle_4_deg 13.503 r_dihedral_angle_1_deg 5.063 r_long_range_B_refined 4.52 r_long_range_B_other 4.517 r_mcangle_it 3.964 r_mcangle_other 3.963
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.122 r_sphericity_free 29.549 r_sphericity_bonded 17.44 r_dihedral_angle_3_deg 14.05 r_dihedral_angle_4_deg 13.503 r_dihedral_angle_1_deg 5.063 r_long_range_B_refined 4.52 r_long_range_B_other 4.517 r_mcangle_it 3.964 r_mcangle_other 3.963 r_scangle_other 3.564 r_mcbond_it 2.954 r_mcbond_other 2.954 r_scbond_it 2.789 r_scbond_other 2.789 r_rigid_bond_restr 1.072 r_angle_refined_deg 0.868 r_angle_other_deg 0.719 r_chiral_restr 0.049 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 367 Heterogen Atoms 180
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing