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crystal structures of RipN from Ralstonia solanacearum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 22YZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 287 0.1 M sodium cacodylate pH 6.1, 0.2 M magnesium acetate, 20% PEG 8000, 10 mM magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.35 47.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.355 α = 90 b = 127.355 β = 90 c = 104.917 γ = 120
Symmetry Space Group P 32 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 PILATUS 6M 2019-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97930 SSRF BL18U1
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 2.278 50 100 1 16.8 11.9 45219
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 2.278 2.32 0.96
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 2.278 20 38540 2025 89.66 0.26555 0.26426 0.2667 0.29018 0.297 RANDOM 36.751
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] 0.65 0.32 0.65 -2.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 21.181 r_long_range_B_refined 6.685 r_long_range_B_other 6.665 r_dihedral_angle_1_deg 5.069 r_scangle_other 4.03 r_mcangle_it 3.934 r_mcangle_other 3.933 r_dihedral_angle_2_deg 2.939 r_mcbond_it 2.612 r_mcbond_other 2.607
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 21.181 r_long_range_B_refined 6.685 r_long_range_B_other 6.665 r_dihedral_angle_1_deg 5.069 r_scangle_other 4.03 r_mcangle_it 3.934 r_mcangle_other 3.933 r_dihedral_angle_2_deg 2.939 r_mcbond_it 2.612 r_mcbond_other 2.607 r_scbond_it 2.581 r_scbond_other 2.581 r_angle_refined_deg 1.543 r_angle_other_deg 0.581 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 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 5505 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement autoPROC data processing autoPX data reduction PHASER phasing