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OleP-oleandolide(DEO) in high salt crystallization conditions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MNS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 4 M Sodium Formate (HCOONa)
Crystal Properties Matthews coefficient Solvent content 3.1 60.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 247.469 α = 90 b = 111.215 β = 129.39 c = 159.203 γ = 90
Symmetry Space Group C 1 2 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 DECTRIS PILATUS3 2M 2015-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.97 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.2 37.73 98.9 0.056 0.99 12.1 3.41 168218
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.33 1.12 0.51
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 5MNS 2.2 37.73 159658 8476 99.46 0.19026 0.18741 0.1922 0.24313 0.2451 RANDOM 60.964
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] 0.06 -0.09 -0.67 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.393 r_dihedral_angle_3_deg 21.241 r_dihedral_angle_4_deg 20.973 r_long_range_B_other 7.972 r_long_range_B_refined 7.971 r_dihedral_angle_1_deg 7.933 r_scangle_other 4.822 r_mcangle_it 4.178 r_mcangle_other 4.178 r_scbond_it 3.203
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.393 r_dihedral_angle_3_deg 21.241 r_dihedral_angle_4_deg 20.973 r_long_range_B_other 7.972 r_long_range_B_refined 7.971 r_dihedral_angle_1_deg 7.933 r_scangle_other 4.822 r_mcangle_it 4.178 r_mcangle_other 4.178 r_scbond_it 3.203 r_scbond_other 3.202 r_mcbond_it 2.684 r_mcbond_other 2.684 r_angle_refined_deg 2.163 r_angle_other_deg 1.465 r_chiral_restr 0.221 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_gen_planes_other 0.006 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18491 Nucleic Acid Atoms Solvent Atoms 763 Heterogen Atoms 782
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing