☰ Navigation Tabs
Structure of the complex of type 1 ribosome inactivating protein from Momordica balsamina with N-acetylglucosamine at 1.98 Angstrom resolution using crystals grown in different conditions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QGJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 298 100mM sodium phosphate,
14% PEG 6000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.39 48.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.148 α = 90 b = 130.148 β = 90 c = 39.693 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD MARMOSAIC 225 mm CCD mirrors 2014-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.98 65.08 100 0.088 29.13 3.7 15675 15675 40.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 2.01 85.4 0.674 1.5 3.5 740
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 4QGJ 1.98 65.07 15675 14870 801 89.77 0.17171 0.17171 0.16834 0.1687 0.21877 0.2215 RANDOM 50.294
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] -1.78 -0.89 -1.78 5.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.417 r_dihedral_angle_4_deg 18.921 r_dihedral_angle_3_deg 15.164 r_long_range_B_refined 9.47 r_long_range_B_other 9.292 r_scangle_other 7.162 r_dihedral_angle_1_deg 5.777 r_mcangle_other 5.155 r_mcangle_it 5.153 r_scbond_it 4.886
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.417 r_dihedral_angle_4_deg 18.921 r_dihedral_angle_3_deg 15.164 r_long_range_B_refined 9.47 r_long_range_B_other 9.292 r_scangle_other 7.162 r_dihedral_angle_1_deg 5.777 r_mcangle_other 5.155 r_mcangle_it 5.153 r_scbond_it 4.886 r_scbond_other 4.862 r_mcbond_it 3.823 r_mcbond_other 3.823 r_angle_refined_deg 1.626 r_angle_other_deg 0.843 r_chiral_restr 0.093 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1911 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 41
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling