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yCP in complex with Omuralide
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 = 135.96 α = 90 b = 301.96 β = 113.14 c = 145.05 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 2.9 30 90.3 0.089 12.6 237133 214131 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 2.9 3 92.7 0.543 2.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1RYP 2.9 15 214131 203424 10707 90.43 0.183 0.18053 0.1791 0.20786 0.1799 RANDOM 57.943
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] 3.16 -0.64 -4.86 1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.961 r_sphericity_free 26.297 r_sphericity_bonded 14.245 r_dihedral_angle_3_deg 13.766 r_dihedral_angle_4_deg 12.816 r_dihedral_angle_1_deg 4.971 r_long_range_B_refined 3.299 r_long_range_B_other 3.286 r_mcangle_it 2.775 r_mcangle_other 2.775
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.961 r_sphericity_free 26.297 r_sphericity_bonded 14.245 r_dihedral_angle_3_deg 13.766 r_dihedral_angle_4_deg 12.816 r_dihedral_angle_1_deg 4.971 r_long_range_B_refined 3.299 r_long_range_B_other 3.286 r_mcangle_it 2.775 r_mcangle_other 2.775 r_scangle_other 2.63 r_scbond_it 2.116 r_scbond_other 2.116 r_mcbond_it 2.088 r_mcbond_other 2.088 r_angle_refined_deg 0.842 r_rigid_bond_restr 0.8 r_angle_other_deg 0.784 r_chiral_restr 0.048 r_bond_refined_d 0.004 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 49366 Nucleic Acid Atoms Solvent Atoms 329 Heterogen Atoms 101
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing