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yCP beta5-A50V 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 = 135.35 α = 90 b = 299.86 β = 112.95 c = 144.82 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 2012-10-20 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 96.2 0.086 10.4 234397 225490 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 97.8 0.495 2.9
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 225490 214215 11275 96.33 0.191 0.18818 0.1867 0.1908 0.21636 0.2204 RANDOM 60.888
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] 3.42 -1.46 -4.94 1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.139 r_sphericity_free 28.57 r_sphericity_bonded 17.648 r_dihedral_angle_3_deg 13.878 r_dihedral_angle_4_deg 13.396 r_dihedral_angle_1_deg 5.065 r_long_range_B_refined 3.782 r_long_range_B_other 3.772 r_mcangle_it 3.225 r_mcangle_other 3.225
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.139 r_sphericity_free 28.57 r_sphericity_bonded 17.648 r_dihedral_angle_3_deg 13.878 r_dihedral_angle_4_deg 13.396 r_dihedral_angle_1_deg 5.065 r_long_range_B_refined 3.782 r_long_range_B_other 3.772 r_mcangle_it 3.225 r_mcangle_other 3.225 r_scangle_other 2.996 r_mcbond_it 2.424 r_mcbond_other 2.424 r_scbond_it 2.399 r_scbond_other 2.399 r_rigid_bond_restr 1.34 r_angle_refined_deg 0.844 r_angle_other_deg 0.682 r_chiral_restr 0.048 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 49370 Nucleic Acid Atoms Solvent Atoms 335 Heterogen Atoms 181
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing