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yCP beta5-C63F mutant in complex with carfilzomib
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RYP pdb entry 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 = 137.68 α = 90 b = 300.99 β = 112.96 c = 145.99 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 97.9 0.069 12.5 218048 213469 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 0.42 2.8
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 pdb entry 1RYP 3 15 213467 202793 10674 98.07 0.17648 0.17449 0.1816 0.21444 0.2175 RANDOM 79.627
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] 5.32 -0.61 -10.89 4.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.046 r_sphericity_free 31.271 r_sphericity_bonded 20.994 r_dihedral_angle_3_deg 14.012 r_dihedral_angle_4_deg 13.553 r_long_range_B_refined 5.297 r_long_range_B_other 5.295 r_dihedral_angle_1_deg 4.979 r_mcangle_it 4.733 r_mcangle_other 4.733
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.046 r_sphericity_free 31.271 r_sphericity_bonded 20.994 r_dihedral_angle_3_deg 14.012 r_dihedral_angle_4_deg 13.553 r_long_range_B_refined 5.297 r_long_range_B_other 5.295 r_dihedral_angle_1_deg 4.979 r_mcangle_it 4.733 r_mcangle_other 4.733 r_scangle_other 4.258 r_mcbond_it 3.545 r_mcbond_other 3.545 r_scbond_it 3.369 r_scbond_other 3.369 r_rigid_bond_restr 0.925 r_angle_refined_deg 0.867 r_angle_other_deg 0.78 r_chiral_restr 0.049 r_bond_refined_d 0.005 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 49305 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 368
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing