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yCP beta5-C52F 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 = 135.2 α = 90 b = 299.25 β = 113.01 c = 144.85 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 2013-02-09 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 3 30 97.5 0.098 10.9 211036 205760 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 3 3.1 99.4 0.469 3.1
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 3 15 205759 195471 10288 97.62 0.18268 0.18084 0.1861 0.2178 0.2187 RANDOM 62.141
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] 4.42 -0.46 -5.93 1.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.283 r_sphericity_free 29.447 r_sphericity_bonded 17.328 r_dihedral_angle_3_deg 13.681 r_dihedral_angle_4_deg 13.21 r_dihedral_angle_1_deg 5.15 r_long_range_B_refined 3.857 r_long_range_B_other 3.845 r_mcangle_it 3.35 r_mcangle_other 3.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.283 r_sphericity_free 29.447 r_sphericity_bonded 17.328 r_dihedral_angle_3_deg 13.681 r_dihedral_angle_4_deg 13.21 r_dihedral_angle_1_deg 5.15 r_long_range_B_refined 3.857 r_long_range_B_other 3.845 r_mcangle_it 3.35 r_mcangle_other 3.35 r_scangle_other 3.046 r_mcbond_it 2.504 r_mcbond_other 2.504 r_scbond_it 2.44 r_scbond_other 2.44 r_angle_refined_deg 0.852 r_rigid_bond_restr 0.78 r_angle_other_deg 0.704 r_chiral_restr 0.048 r_bond_refined_d 0.004 r_bond_other_d 0.002 r_gen_planes_refined 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 49376 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms 179
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing