☰ Navigation Tabs
Atomic resolution structure of cucurmosin, a novel type 1 RIP from the sarcocarp of Cucurbita moschata
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TCS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.9 298 100 mM phosphate buffer, 20% PEG6000, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 5.90
Crystal Properties Matthews coefficient Solvent content 2.25 45.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.763 α = 90 b = 58.782 β = 90 c = 99.523 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 93 CCD MARMOSAIC 325 mm CCD MIRRORS 2002-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1 50 84 0.108 0.108 22.9 7.4 111623 9.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1 1.04 40.6 0.393 0.393 1.3 2.1
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1TCS 1 38.52 105926 105926 5611 84 0.172 0.171 0.179 RANDOM 9.72
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 0.1 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.425 r_dihedral_angle_4_deg 17.94 r_dihedral_angle_3_deg 9.785 r_dihedral_angle_1_deg 5.465 r_sphericity_free 2.944 r_scangle_it 2.448 r_sphericity_bonded 2.1 r_scbond_it 1.863 r_angle_refined_deg 1.498 r_angle_other_deg 1.476
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.425 r_dihedral_angle_4_deg 17.94 r_dihedral_angle_3_deg 9.785 r_dihedral_angle_1_deg 5.465 r_sphericity_free 2.944 r_scangle_it 2.448 r_sphericity_bonded 2.1 r_scbond_it 1.863 r_angle_refined_deg 1.498 r_angle_other_deg 1.476 r_mcangle_it 1.345 r_mcbond_it 1.084 r_rigid_bond_restr 1.074 r_mcbond_other 0.376 r_nbd_refined 0.212 r_symmetry_vdw_refined 0.209 r_symmetry_vdw_other 0.193 r_nbd_other 0.176 r_nbtor_refined 0.171 r_symmetry_hbond_refined 0.155 r_chiral_restr 0.121 r_xyhbond_nbd_refined 0.112 r_nbtor_other 0.085 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1907 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 95
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing