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yCP 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 = 135.81 α = 90 b = 298.69 β = 112.69 c = 145.7 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 2013-03-16 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 96.9 0.082 10.4 262363 254230 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 0.544 2.3
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 254230 241518 12712 97.04 0.191 0.18861 0.18716 0.1914 0.21636 0.2192 RANDOM 61.124
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] 1.91 -0.67 -4.49 2.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.036 r_sphericity_free 25.327 r_sphericity_bonded 16.017 r_dihedral_angle_3_deg 14.084 r_dihedral_angle_4_deg 13.403 r_dihedral_angle_1_deg 5.028 r_long_range_B_refined 3.774 r_long_range_B_other 3.769 r_mcangle_it 3.257 r_mcangle_other 3.257
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.036 r_sphericity_free 25.327 r_sphericity_bonded 16.017 r_dihedral_angle_3_deg 14.084 r_dihedral_angle_4_deg 13.403 r_dihedral_angle_1_deg 5.028 r_long_range_B_refined 3.774 r_long_range_B_other 3.769 r_mcangle_it 3.257 r_mcangle_other 3.257 r_scangle_other 2.989 r_mcbond_it 2.42 r_mcbond_other 2.42 r_scbond_it 2.345 r_scbond_other 2.345 r_rigid_bond_restr 0.936 r_angle_refined_deg 0.865 r_angle_other_deg 0.762 r_chiral_restr 0.049 r_bond_refined_d 0.005 r_bond_other_d 0.002 r_gen_planes_refined 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 49295 Nucleic Acid Atoms Solvent Atoms 332 Heterogen Atoms 371
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing