☰ Navigation Tabs
Crystal structure and anti-tumor activity of LZ-8 from the fungus Ganoderma lucidium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OSY PDB entry 1OSY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 289 0.1M Tris, 1.75M ammonium sulfate, 6.4% polyethylene glycol 400, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289.0K
Crystal Properties Matthews coefficient Solvent content 2.66 53.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.19 α = 90 b = 86.99 β = 90 c = 92.13 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH 2007-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54179
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 2.1 20 98 0.125 4.8 15951
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 2.1 2.21 93.6 0.302
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 PDB entry 1OSY 2.1 20 15140 800 97.98 0.22218 0.22096 0.2233 0.24552 0.2479 RANDOM 13.534
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] -2.56 4.1 -1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.561 r_dihedral_angle_3_deg 12.495 r_dihedral_angle_4_deg 8.026 r_dihedral_angle_1_deg 6.174 r_scangle_it 1.253 r_angle_refined_deg 1.054 r_scbond_it 0.807 r_mcangle_it 0.525 r_mcbond_it 0.306 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.561 r_dihedral_angle_3_deg 12.495 r_dihedral_angle_4_deg 8.026 r_dihedral_angle_1_deg 6.174 r_scangle_it 1.253 r_angle_refined_deg 1.054 r_scbond_it 0.807 r_mcangle_it 0.525 r_mcbond_it 0.306 r_nbtor_refined 0.304 r_nbd_refined 0.175 r_symmetry_vdw_refined 0.142 r_xyhbond_nbd_refined 0.103 r_symmetry_hbond_refined 0.091 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1752 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling