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Crystal structure of CmnI
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 20% (w/v) PEG 1000 100 mM Tris base/ Hydrochloric acid pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.7 54.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.888 α = 90 b = 129.52 β = 95.15 c = 61.313 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 CCD RAYONIX MX300HE 2025-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1 NSRRC BL15A1
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 2.17 27.65 98.2 0.056 20.8 3.2 61605
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 2.17 2.25 0.59
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 (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 AlphaFold 2.17 27.65 61605 3301 94.42 0.21644 0.2149 0.2212 0.24552 0.2521 RANDOM 37.752
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] -0.29 0.3 0.67 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.859 r_long_range_B_other 8.971 r_long_range_B_refined 8.899 r_dihedral_angle_2_deg 6.722 r_dihedral_angle_1_deg 6.179 r_scangle_other 4.752 r_mcangle_it 4.232 r_mcangle_other 4.232 r_scbond_it 2.823 r_scbond_other 2.823
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.859 r_long_range_B_other 8.971 r_long_range_B_refined 8.899 r_dihedral_angle_2_deg 6.722 r_dihedral_angle_1_deg 6.179 r_scangle_other 4.752 r_mcangle_it 4.232 r_mcangle_other 4.232 r_scbond_it 2.823 r_scbond_other 2.823 r_mcbond_it 2.572 r_mcbond_other 2.572 r_angle_refined_deg 1.292 r_angle_other_deg 0.471 r_chiral_restr 0.059 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6626 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 102
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing Coot model building