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yCP in complex with bortezomib
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 = 134.91 α = 90 b = 300.21 β = 112.85 c = 144.76 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 2013-06-08 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 92.8 0.077 10.5 259911 241198 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 95.4 0.513 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 (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 2.8 15 241197 229137 12060 92.93 0.18845 0.18706 0.1929 0.21465 0.2189 RANDOM 66.893
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] 4.3 -0.97 -6.88 2.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.268 r_sphericity_free 28.503 r_sphericity_bonded 17.574 r_dihedral_angle_3_deg 14.124 r_dihedral_angle_4_deg 13.941 r_dihedral_angle_1_deg 5.122 r_long_range_B_refined 4.261 r_long_range_B_other 4.247 r_mcangle_it 3.757 r_mcangle_other 3.757
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.268 r_sphericity_free 28.503 r_sphericity_bonded 17.574 r_dihedral_angle_3_deg 14.124 r_dihedral_angle_4_deg 13.941 r_dihedral_angle_1_deg 5.122 r_long_range_B_refined 4.261 r_long_range_B_other 4.247 r_mcangle_it 3.757 r_mcangle_other 3.757 r_scangle_other 3.321 r_mcbond_it 2.778 r_mcbond_other 2.778 r_scbond_it 2.637 r_scbond_other 2.637 r_rigid_bond_restr 0.909 r_angle_refined_deg 0.874 r_angle_other_deg 0.71 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 49366 Nucleic Acid Atoms Solvent Atoms 357 Heterogen Atoms 180
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing