☰ Navigation Tabs
yCP beta5-A50V 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 = 135.79 α = 90 b = 300.31 β = 112.83 c = 146.09 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 2012-10-20 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 97.3 0.081 9.8 264122 256991 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 98.8 0.489 2.6
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 2.8 15 256990 244140 12850 97.42 0.18 0.17736 0.17549 0.1813 0.21293 0.2143 RANDOM 68.921
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] 4.61 0.97 -7.59 1.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.721 r_sphericity_free 28.611 r_dihedral_angle_3_deg 15.242 r_dihedral_angle_4_deg 15.214 r_sphericity_bonded 14.484 r_dihedral_angle_1_deg 5.469 r_long_range_B_refined 4.082 r_long_range_B_other 4.075 r_mcangle_it 3.593 r_mcangle_other 3.593
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.721 r_sphericity_free 28.611 r_dihedral_angle_3_deg 15.242 r_dihedral_angle_4_deg 15.214 r_sphericity_bonded 14.484 r_dihedral_angle_1_deg 5.469 r_long_range_B_refined 4.082 r_long_range_B_other 4.075 r_mcangle_it 3.593 r_mcangle_other 3.593 r_scangle_other 3.317 r_mcbond_it 2.738 r_mcbond_other 2.738 r_scbond_it 2.7 r_scbond_other 2.7 r_rigid_bond_restr 1.189 r_angle_refined_deg 0.941 r_angle_other_deg 0.821 r_chiral_restr 0.053 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 49291 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 285
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing