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RMI1-RMI2 bound to cyclic peptide L3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MXN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 1.8 M sodium phosphate monobasic monohydrate / potassium phosphate dibasic pH 5.0
Crystal Properties Matthews coefficient Solvent content 2.77 55.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 189.15 α = 90 b = 50.622 β = 118.047 c = 181.221 γ = 90
Symmetry Space Group C 1 2 1
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 EIGER X 16M 2022-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.35 48.272 99.2 0.983 5.6 3.5 63378
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.41 0.406 1.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.35 48.272 63377 3158 99.047 0.206 0.2035 0.2036 0.2467 0.2475 40.057
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] -0.362 0.33 -1.142 0.735
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.941 r_dihedral_angle_6_deg 15.875 r_dihedral_angle_2_deg 15.841 r_lrange_it 8.461 r_lrange_other 8.459 r_dihedral_angle_1_deg 7.41 r_scangle_it 6.311 r_scangle_other 6.31 r_scbond_it 4.073 r_scbond_other 4.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.941 r_dihedral_angle_6_deg 15.875 r_dihedral_angle_2_deg 15.841 r_lrange_it 8.461 r_lrange_other 8.459 r_dihedral_angle_1_deg 7.41 r_scangle_it 6.311 r_scangle_other 6.31 r_scbond_it 4.073 r_scbond_other 4.073 r_mcangle_it 3.951 r_mcangle_other 3.951 r_mcbond_other 2.516 r_mcbond_it 2.515 r_angle_refined_deg 1.941 r_angle_other_deg 0.616 r_nbd_refined 0.223 r_nbd_other 0.213 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.185 r_symmetry_xyhbond_nbd_refined 0.176 r_symmetry_nbd_refined 0.157 r_xyhbond_nbd_refined 0.142 r_ncsr_local_group_4 0.14 r_ncsr_local_group_14 0.13 r_ncsr_local_group_10 0.129 r_ncsr_local_group_16 0.128 r_ncsr_local_group_5 0.124 r_ncsr_local_group_12 0.122 r_ncsr_local_group_18 0.122 r_ncsr_local_group_9 0.112 r_ncsr_local_group_6 0.106 r_ncsr_local_group_17 0.1 r_ncsr_local_group_2 0.099 r_ncsr_local_group_13 0.098 r_ncsr_local_group_11 0.089 r_symmetry_nbtor_other 0.088 r_ncsr_local_group_8 0.085 r_ncsr_local_group_1 0.084 r_ncsr_local_group_3 0.082 r_chiral_restr 0.079 r_ncsr_local_group_7 0.079 r_ncsr_local_group_15 0.051 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_symmetry_xyhbond_nbd_other 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9139 Nucleic Acid Atoms Solvent Atoms 289 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing