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yCP beta5-M45A 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 = 137.49 α = 90 b = 299.73 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 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 2.8 30 98 0.078 11.5 265266 259961 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 2.8 2.9 99.2 0.545 2.8
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 2.8 15 259961 246963 12998 98.1 0.18945 0.18773 0.1923 0.22235 0.2257 RANDOM 71.99
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] 3.3 -0.45 -7.51 3.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.078 r_sphericity_free 30.162 r_sphericity_bonded 19.833 r_dihedral_angle_3_deg 14.17 r_dihedral_angle_4_deg 13.935 r_dihedral_angle_1_deg 5.052 r_long_range_B_refined 4.518 r_long_range_B_other 4.511 r_mcangle_it 3.948 r_mcangle_other 3.948
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.078 r_sphericity_free 30.162 r_sphericity_bonded 19.833 r_dihedral_angle_3_deg 14.17 r_dihedral_angle_4_deg 13.935 r_dihedral_angle_1_deg 5.052 r_long_range_B_refined 4.518 r_long_range_B_other 4.511 r_mcangle_it 3.948 r_mcangle_other 3.948 r_scangle_other 3.671 r_mcbond_it 2.982 r_mcbond_other 2.981 r_scbond_it 2.902 r_scbond_other 2.902 r_rigid_bond_restr 1.44 r_angle_refined_deg 0.891 r_angle_other_deg 0.807 r_chiral_restr 0.051 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 49198 Nucleic Acid Atoms Solvent Atoms 277 Heterogen Atoms 308
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing