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Crystal structure of a new isoform of ribosome inactivating protein from Momordica balsamina at 1.41 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MRW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.7 298 PEG 6000, 0.1M Sodium Phosphate
Crystal Properties Matthews coefficient Solvent content 2.4 48.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.303 α = 90 b = 130.303 β = 90 c = 39.853 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 100 PIXEL DECTRIS EIGER2 X 9M 2023-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.87313 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.408 37.644 99.8 0.034 0.042 0.025 0.999 18.1 5.2 48750 21.5
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 1.41 1.43 98.9 1.284 0.476 1 5.4
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3MRW 1.408 37.644 48641 2465 99.529 0.18 0.1788 0.187 0.2035 0.2108 22.916
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] -0.356 -0.178 -0.356 1.156
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.716 r_dihedral_angle_2_deg 13.202 r_dihedral_angle_3_deg 13.081 r_dihedral_angle_1_deg 5.867 r_lrange_it 5.756 r_lrange_other 5.625 r_scangle_it 4.913 r_scangle_other 4.911 r_scbond_it 3.549 r_scbond_other 3.549
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.716 r_dihedral_angle_2_deg 13.202 r_dihedral_angle_3_deg 13.081 r_dihedral_angle_1_deg 5.867 r_lrange_it 5.756 r_lrange_other 5.625 r_scangle_it 4.913 r_scangle_other 4.911 r_scbond_it 3.549 r_scbond_other 3.549 r_mcangle_it 2.776 r_mcangle_other 2.776 r_mcbond_it 2.128 r_mcbond_other 2.128 r_angle_refined_deg 1.894 r_angle_other_deg 0.667 r_symmetry_nbd_refined 0.446 r_nbd_other 0.251 r_nbd_refined 0.245 r_symmetry_xyhbond_nbd_other 0.219 r_xyhbond_nbd_refined 0.207 r_symmetry_nbd_other 0.203 r_nbtor_refined 0.182 r_symmetry_xyhbond_nbd_refined 0.152 r_chiral_restr 0.097 r_symmetry_nbtor_other 0.092 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1920 Nucleic Acid Atoms Solvent Atoms 293 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling MOLREP phasing autoPROC data processing Coot model building