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X-ray Sequence and Crystal Structure of Luffaculin 1, a Novel Type 1 Ribosome-inactivating Protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other a homology model built based on the sequence luffin a
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 298 28% (w/v) PEG 6000, 0.1M citrate buffer(containing 0.02% (w/v) sodium azide)', pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.77 55.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.135 α = 89.07 b = 46.813 β = 80.01 c = 83.571 γ = 72.14
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MAR CCD 130 mm mirrors 2005-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.05 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 1.4 33.9 86.7 0.03 0.115 21.8 1.9 94795 2 2 18.964
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 1.4 1.436 62 0.03 0.115 4.6 1.7 94795
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT a homology model built based on the sequence luffin a 1.4 33.9 2 2 94795 4750 86.7 0.21405 0.21313 0.21313 0.2149 0.23157 RANDOM 18.964
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] -0.69 -0.42 0.46 1.67 -1.05 -0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.287 r_dihedral_angle_4_deg 20.006 r_dihedral_angle_3_deg 11.308 r_dihedral_angle_1_deg 4.628 r_scangle_it 2.346 r_scbond_it 1.554 r_angle_refined_deg 1.153 r_mcangle_it 0.965 r_mcbond_it 0.577 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.287 r_dihedral_angle_4_deg 20.006 r_dihedral_angle_3_deg 11.308 r_dihedral_angle_1_deg 4.628 r_scangle_it 2.346 r_scbond_it 1.554 r_angle_refined_deg 1.153 r_mcangle_it 0.965 r_mcbond_it 0.577 r_nbtor_refined 0.307 r_nbd_refined 0.214 r_symmetry_vdw_refined 0.153 r_xyhbond_nbd_refined 0.133 r_symmetry_hbond_refined 0.101 r_chiral_restr 0.077 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3600 Nucleic Acid Atoms Solvent Atoms 490 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing