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yCP beta5-M45A 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 = 135.55 α = 90 b = 300.11 β = 113 c = 145.15 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 3 30 99.1 0.082 13.2 212666 210752 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 3 3.1 99.4 0.475 2.4
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 3 15 210751 200213 10538 99.24 0.174 0.17086 0.1693 0.1754 0.20062 0.2043 RANDOM 71.373
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] 3.6 -0.17 -7.94 3.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.004 r_sphericity_free 27.437 r_sphericity_bonded 18.895 r_dihedral_angle_3_deg 13.954 r_dihedral_angle_4_deg 13.488 r_dihedral_angle_1_deg 5.035 r_long_range_B_refined 4.625 r_long_range_B_other 4.621 r_mcangle_it 4.034 r_mcangle_other 4.034
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.004 r_sphericity_free 27.437 r_sphericity_bonded 18.895 r_dihedral_angle_3_deg 13.954 r_dihedral_angle_4_deg 13.488 r_dihedral_angle_1_deg 5.035 r_long_range_B_refined 4.625 r_long_range_B_other 4.621 r_mcangle_it 4.034 r_mcangle_other 4.034 r_scangle_other 3.686 r_mcbond_it 2.989 r_mcbond_other 2.989 r_scbond_it 2.9 r_scbond_other 2.899 r_rigid_bond_restr 0.924 r_angle_refined_deg 0.872 r_angle_other_deg 0.764 r_chiral_restr 0.049 r_bond_refined_d 0.005 r_bond_other_d 0.003 r_gen_planes_refined 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 49289 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 369
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing