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yCP beta5-A49T-A50V-double mutant in complex with bortezomib
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 = 136.93 α = 90 b = 301.26 β = 113.16 c = 145.61 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 2012-05-13 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 97.6 0.077 11.8 239156 233416 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 99.1 0.512 2.6
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 2.9 15 233415 221744 11671 97.72 0.183 0.17952 0.17785 0.1831 0.21142 0.214 RANDOM 72.647
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] 4.34 0.53 -7.95 2.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.257 r_sphericity_free 28.218 r_sphericity_bonded 20.284 r_dihedral_angle_3_deg 14.109 r_dihedral_angle_4_deg 13.941 r_dihedral_angle_1_deg 5.036 r_long_range_B_refined 4.612 r_long_range_B_other 4.608 r_mcangle_it 4.059 r_mcangle_other 4.059
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.257 r_sphericity_free 28.218 r_sphericity_bonded 20.284 r_dihedral_angle_3_deg 14.109 r_dihedral_angle_4_deg 13.941 r_dihedral_angle_1_deg 5.036 r_long_range_B_refined 4.612 r_long_range_B_other 4.608 r_mcangle_it 4.059 r_mcangle_other 4.059 r_scangle_other 3.803 r_mcbond_it 3.039 r_mcbond_other 3.039 r_scbond_it 3.001 r_scbond_other 3.001 r_rigid_bond_restr 1.2 r_angle_refined_deg 0.857 r_angle_other_deg 0.706 r_chiral_restr 0.049 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 49372 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 180
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing