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yCP beta5-C52F mutant 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 = 136.25 α = 90 b = 301.24 β = 113.16 c = 144.33 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 2.8 30 97.5 0.087 11.1 261898 255351 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 97 0.505 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 2.8 15 255351 242583 12768 97.59 0.188 0.1852 0.18389 0.1894 0.20992 0.2129 RANDOM 59.818
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] 2.54 -0.7 -4.6 1.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.63 r_sphericity_free 26.022 r_sphericity_bonded 16.45 r_dihedral_angle_3_deg 13.58 r_dihedral_angle_4_deg 12.486 r_dihedral_angle_1_deg 4.918 r_long_range_B_refined 3.828 r_long_range_B_other 3.823 r_mcangle_it 3.302 r_mcangle_other 3.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.63 r_sphericity_free 26.022 r_sphericity_bonded 16.45 r_dihedral_angle_3_deg 13.58 r_dihedral_angle_4_deg 12.486 r_dihedral_angle_1_deg 4.918 r_long_range_B_refined 3.828 r_long_range_B_other 3.823 r_mcangle_it 3.302 r_mcangle_other 3.302 r_scangle_other 3.078 r_mcbond_it 2.447 r_mcbond_other 2.447 r_scbond_it 2.422 r_scbond_other 2.422 r_rigid_bond_restr 1.204 r_angle_refined_deg 0.846 r_angle_other_deg 0.793 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 49376 Nucleic Acid Atoms Solvent Atoms 343 Heterogen Atoms 103
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing