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yCP beta5-M45A mutant 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 = 136.89 α = 90 b = 299.88 β = 112.96 c = 145.9 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 2.8 30 96.9 0.075 12 265130 256911 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 97.9 0.55 2.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1RYP 2.8 15 256910 244064 12846 96.99 0.18863 0.18724 0.21474 0.2028 RANDOM 68.355
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] 3.01 -0.72 -6.25 2.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.04 r_sphericity_free 26.347 r_sphericity_bonded 18.843 r_dihedral_angle_3_deg 13.807 r_dihedral_angle_4_deg 13.515 r_dihedral_angle_1_deg 4.984 r_long_range_B_refined 4.052 r_long_range_B_other 4.042 r_mcangle_it 3.532 r_mcangle_other 3.532
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.04 r_sphericity_free 26.347 r_sphericity_bonded 18.843 r_dihedral_angle_3_deg 13.807 r_dihedral_angle_4_deg 13.515 r_dihedral_angle_1_deg 4.984 r_long_range_B_refined 4.052 r_long_range_B_other 4.042 r_mcangle_it 3.532 r_mcangle_other 3.532 r_scangle_other 3.245 r_mcbond_it 2.68 r_mcbond_other 2.68 r_scbond_it 2.606 r_scbond_other 2.606 r_rigid_bond_restr 0.889 r_angle_refined_deg 0.853 r_angle_other_deg 0.697 r_chiral_restr 0.048 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 49360 Nucleic Acid Atoms Solvent Atoms 331 Heterogen Atoms 181
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing