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yCP beta5-M45I 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 = 136.62 α = 90 b = 299.64 β = 112.88 c = 145.75 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 97.4 0.09 12.7 214982 209392 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 99.1 0.48 3.4
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 (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 209392 198922 10470 97.48 0.17702 0.17565 0.1808 0.20279 0.2056 RANDOM 61.674
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] 2.8 -0.2 -5.94 2.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.67 r_sphericity_free 27.275 r_sphericity_bonded 16.939 r_dihedral_angle_3_deg 13.62 r_dihedral_angle_4_deg 13.084 r_dihedral_angle_1_deg 4.94 r_long_range_B_refined 3.773 r_long_range_B_other 3.771 r_mcangle_it 3.265 r_mcangle_other 3.265
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.67 r_sphericity_free 27.275 r_sphericity_bonded 16.939 r_dihedral_angle_3_deg 13.62 r_dihedral_angle_4_deg 13.084 r_dihedral_angle_1_deg 4.94 r_long_range_B_refined 3.773 r_long_range_B_other 3.771 r_mcangle_it 3.265 r_mcangle_other 3.265 r_scangle_other 2.989 r_mcbond_it 2.434 r_mcbond_other 2.434 r_scbond_it 2.372 r_scbond_other 2.372 r_angle_refined_deg 0.872 r_rigid_bond_restr 0.84 r_angle_other_deg 0.785 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 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 49295 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms 371
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing