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yCP beta5-M45I 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
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 = 137.16 α = 90 b = 299.33 β = 113.09 c = 145.39 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 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 2.7 30 98.8 0.079 12.9 294467 290933 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 2.7 2.8 99.4 0.541 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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1RYP 2.7 15 290933 276386 14547 98.93 0.198 0.19589 0.1947 0.21865 0.2056 RANDOM 64.59
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] 2.37 -0.35 -6.76 3.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.681 r_sphericity_free 26.194 r_sphericity_bonded 20.569 r_dihedral_angle_3_deg 13.595 r_dihedral_angle_4_deg 13.108 r_dihedral_angle_1_deg 4.967 r_long_range_B_refined 3.435 r_long_range_B_other 3.411 r_mcangle_it 3.001 r_mcangle_other 3.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.681 r_sphericity_free 26.194 r_sphericity_bonded 20.569 r_dihedral_angle_3_deg 13.595 r_dihedral_angle_4_deg 13.108 r_dihedral_angle_1_deg 4.967 r_long_range_B_refined 3.435 r_long_range_B_other 3.411 r_mcangle_it 3.001 r_mcangle_other 3.001 r_scangle_other 2.694 r_mcbond_it 2.271 r_mcbond_other 2.271 r_scbond_it 2.175 r_scbond_other 2.174 r_rigid_bond_restr 1.173 r_angle_refined_deg 0.902 r_angle_other_deg 0.82 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 49296 Nucleic Acid Atoms Solvent Atoms 449 Heterogen Atoms 309
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing