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Structure of a 150% lengthened variant of the E. coli ROP protein
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, SITTING DROP 5.2 290 200 mM Na Phosphate 30% PEG 300
Crystal Properties Matthews coefficient Solvent content 2.1 41.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.253 α = 90 b = 43.253 β = 90 c = 84.158 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 EIGER X 16M 2023-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X17B1 0.97934 NSLS X17B1
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 1.75 22.45 99.7 0.121 0.129 0.044 0.996 10.9 7.8 17737
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 96.7 0.407 0.458 0.205 0.817 4.7
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 (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 1.75 22.45 16826 880 99.72 0.20211 0.1994 0.234 0.25602 0.2958 RANDOM 29.644
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] -5.09 -5.09 10.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.004 r_dihedral_angle_3_deg 16.79 r_dihedral_angle_4_deg 11.152 r_long_range_B_refined 9.698 r_dihedral_angle_1_deg 4.956 r_scbond_it 2.631 r_angle_refined_deg 2.049 r_mcangle_it 1.957 r_mcbond_it 1.463 r_chiral_restr 0.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.004 r_dihedral_angle_3_deg 16.79 r_dihedral_angle_4_deg 11.152 r_long_range_B_refined 9.698 r_dihedral_angle_1_deg 4.956 r_scbond_it 2.631 r_angle_refined_deg 2.049 r_mcangle_it 1.957 r_mcbond_it 1.463 r_chiral_restr 0.126 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1362 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing autoPROC data reduction