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yCP beta5-A49V 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 = 135.76 α = 90 b = 300.17 β = 112.96 c = 144.96 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 2012-05-13 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 97.2 0.084 9.2 254320 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 0.482 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 (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 254319 241603 12716 97.32 0.18188 0.18054 0.1853 0.20748 0.2101 RANDOM 64.466
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] 2.64 -0.16 -6.23 2.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.342 r_sphericity_free 28.619 r_sphericity_bonded 16.203 r_dihedral_angle_3_deg 14.733 r_dihedral_angle_4_deg 14.482 r_dihedral_angle_1_deg 5.141 r_long_range_B_refined 3.596 r_long_range_B_other 3.584 r_mcangle_it 3.159 r_mcangle_other 3.159
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.342 r_sphericity_free 28.619 r_sphericity_bonded 16.203 r_dihedral_angle_3_deg 14.733 r_dihedral_angle_4_deg 14.482 r_dihedral_angle_1_deg 5.141 r_long_range_B_refined 3.596 r_long_range_B_other 3.584 r_mcangle_it 3.159 r_mcangle_other 3.159 r_scangle_other 2.884 r_mcbond_it 2.364 r_mcbond_other 2.364 r_scbond_it 2.315 r_scbond_other 2.315 r_rigid_bond_restr 1.635 r_angle_refined_deg 0.902 r_angle_other_deg 0.813 r_chiral_restr 0.052 r_bond_refined_d 0.004 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 49300 Nucleic Acid Atoms Solvent Atoms 332 Heterogen Atoms 285
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing