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yCP beta5-C52F 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 = 136.66 α = 90 b = 300.7 β = 113.22 c = 145.38 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 2013-11-30 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 93.1 0.114 11.7 214885 200058 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 96.1 0.559 3.4
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 1RYP 3 15 200058 190055 10003 93.23 0.18942 0.1879 0.1934 0.21826 0.2231 RANDOM 57.206
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] 3.12 -0.34 -5.81 2.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.102 r_sphericity_free 29.292 r_sphericity_bonded 17.022 r_dihedral_angle_3_deg 14.342 r_dihedral_angle_4_deg 13.962 r_dihedral_angle_1_deg 5.082 r_long_range_B_refined 3.685 r_long_range_B_other 3.671 r_mcangle_it 3.147 r_mcangle_other 3.147
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.102 r_sphericity_free 29.292 r_sphericity_bonded 17.022 r_dihedral_angle_3_deg 14.342 r_dihedral_angle_4_deg 13.962 r_dihedral_angle_1_deg 5.082 r_long_range_B_refined 3.685 r_long_range_B_other 3.671 r_mcangle_it 3.147 r_mcangle_other 3.147 r_scangle_other 2.929 r_mcbond_it 2.344 r_mcbond_other 2.344 r_scbond_it 2.309 r_scbond_other 2.309 r_rigid_bond_restr 1.06 r_angle_refined_deg 0.881 r_angle_other_deg 0.78 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 49306 Nucleic Acid Atoms Solvent Atoms 309 Heterogen Atoms 202
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing