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yCP beta5-M45T mutant in complex with the epoxyketone inhibitor ONX 0914
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 = 137.18 α = 90 b = 298.8 β = 113.02 c = 146.83 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 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 97.9 0.097 7.8 216803 212250 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 99.1 0.468 2.1
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 212249 201636 10613 98.05 0.17797 0.17599 0.1859 0.21573 0.2242 RANDOM 84.253
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] 6.39 -2.28 -8.54 2.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.933 r_sphericity_free 31.79 r_sphericity_bonded 24.508 r_dihedral_angle_3_deg 14.001 r_dihedral_angle_4_deg 13.684 r_long_range_B_refined 6.165 r_long_range_B_other 6.159 r_mcangle_it 5.481 r_mcangle_other 5.481 r_dihedral_angle_1_deg 4.986
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.933 r_sphericity_free 31.79 r_sphericity_bonded 24.508 r_dihedral_angle_3_deg 14.001 r_dihedral_angle_4_deg 13.684 r_long_range_B_refined 6.165 r_long_range_B_other 6.159 r_mcangle_it 5.481 r_mcangle_other 5.481 r_dihedral_angle_1_deg 4.986 r_scangle_other 4.957 r_mcbond_it 4.063 r_mcbond_other 4.062 r_scbond_it 3.886 r_scbond_other 3.885 r_rigid_bond_restr 1.374 r_angle_refined_deg 0.898 r_angle_other_deg 0.857 r_chiral_restr 0.05 r_bond_refined_d 0.005 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 49276 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 305
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing