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yCP beta5-M45V 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 = 134.9 α = 90 b = 300.78 β = 113.09 c = 145.16 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 2013-09-07 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 2.9 30 95.9 0.072 12.6 234652 225031 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 2.9 3 97.4 0.535 2
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 2.9 15 225031 213779 11252 96.02 0.17716 0.17529 0.1827 0.21271 0.2191 RANDOM 78.791
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] 5.86 0.5 -9.12 2.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.668 r_sphericity_free 29.013 r_sphericity_bonded 21.155 r_dihedral_angle_3_deg 13.428 r_dihedral_angle_4_deg 12.719 r_long_range_B_refined 5.225 r_long_range_B_other 5.223 r_dihedral_angle_1_deg 4.972 r_mcangle_it 4.612 r_mcangle_other 4.612
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.668 r_sphericity_free 29.013 r_sphericity_bonded 21.155 r_dihedral_angle_3_deg 13.428 r_dihedral_angle_4_deg 12.719 r_long_range_B_refined 5.225 r_long_range_B_other 5.223 r_dihedral_angle_1_deg 4.972 r_mcangle_it 4.612 r_mcangle_other 4.612 r_scangle_other 4.172 r_mcbond_it 3.438 r_mcbond_other 3.438 r_scbond_it 3.28 r_scbond_other 3.28 r_rigid_bond_restr 0.996 r_angle_refined_deg 0.832 r_angle_other_deg 0.679 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 49364 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 179
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing