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Crystal structure of RuABA3 from Rutstroemia sp. NJR-2017a WRK4 in complex with FsPP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8ZAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M sodium malonate pH 7.0, 21% PEG 3350, 0.1 M Bis-Tris pH 8.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.765 α = 90 b = 89.475 β = 90 c = 142.712 γ = 90
Symmetry Space Group P 21 21 21
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 Bruker PHOTON III 2023-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 LIQUID ANODE BRUKER METALJET 1.34138
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 2.28 35.03 98.1 0.996 8.5 7.3 27175
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 2.28 2.32 0.792
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 8ZAD 2.28 35.03 27175 1444 93.41 0.18057 0.17689 0.183 0.25018 0.253 RANDOM 36.589
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] 2.65 -2.15 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.481 r_dihedral_angle_3_deg 17.597 r_dihedral_angle_4_deg 16.886 r_long_range_B_refined 6.988 r_long_range_B_other 6.985 r_dihedral_angle_1_deg 6.858 r_scangle_other 5.201 r_mcangle_it 4.726 r_mcangle_other 4.726 r_scbond_it 3.348
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.481 r_dihedral_angle_3_deg 17.597 r_dihedral_angle_4_deg 16.886 r_long_range_B_refined 6.988 r_long_range_B_other 6.985 r_dihedral_angle_1_deg 6.858 r_scangle_other 5.201 r_mcangle_it 4.726 r_mcangle_other 4.726 r_scbond_it 3.348 r_scbond_other 3.335 r_mcbond_it 3.138 r_mcbond_other 3.131 r_angle_refined_deg 1.566 r_angle_other_deg 1.292 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 5451 Nucleic Acid Atoms Solvent Atoms 317 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement SAINT data scaling SAINT data reduction PHASER phasing