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yCP beta5-C63F 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 = 137.21 α = 90 b = 300.81 β = 113.52 c = 145.09 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 2.6 30 98.2 0.066 10.8 329831 323894 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 2.6 2.7 99.4 0.455 2.3
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 2.6 15 323893 307698 16195 98.36 0.201 0.19881 0.19754 0.2032 0.22293 0.2277 RANDOM 67.386
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] 2.78 -1.88 -6.19 3.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.166 r_sphericity_free 27.56 r_sphericity_bonded 19.496 r_dihedral_angle_4_deg 14.128 r_dihedral_angle_3_deg 14.084 r_dihedral_angle_1_deg 5.07 r_long_range_B_refined 3.918 r_long_range_B_other 3.901 r_mcangle_it 3.505 r_mcangle_other 3.505
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.166 r_sphericity_free 27.56 r_sphericity_bonded 19.496 r_dihedral_angle_4_deg 14.128 r_dihedral_angle_3_deg 14.084 r_dihedral_angle_1_deg 5.07 r_long_range_B_refined 3.918 r_long_range_B_other 3.901 r_mcangle_it 3.505 r_mcangle_other 3.505 r_scangle_other 3.012 r_mcbond_it 2.614 r_mcbond_other 2.614 r_scbond_it 2.409 r_scbond_other 2.409 r_rigid_bond_restr 1.171 r_angle_refined_deg 0.893 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 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 49279 Nucleic Acid Atoms Solvent Atoms 455 Heterogen Atoms 310
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing