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SP1746 treated with EDTA, in complex with ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OGI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 287.2 20% PEG3350,0.2 M Potassium sulfate
Crystal Properties Matthews coefficient Solvent content 2.45 49.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.271 α = 90 b = 69.271 β = 90 c = 88.463 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 200K 2024-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.984050 SSRF BL17U1
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 1.6 50.01 100 0.9993 31.97 19.1 32997
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 1.6 1.64 0.8428
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.6 50.01 31263 1678 99.98 0.19407 0.19362 0.20216 0.1857 RANDOM 19.827
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] 0.31 0.15 0.31 -1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.302 r_dihedral_angle_4_deg 22.624 r_dihedral_angle_3_deg 13.203 r_dihedral_angle_1_deg 4.77 r_long_range_B_refined 3.734 r_angle_refined_deg 1.23 r_scbond_it 1.117 r_mcangle_it 1.092 r_mcbond_it 0.663 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.302 r_dihedral_angle_4_deg 22.624 r_dihedral_angle_3_deg 13.203 r_dihedral_angle_1_deg 4.77 r_long_range_B_refined 3.734 r_angle_refined_deg 1.23 r_scbond_it 1.117 r_mcangle_it 1.092 r_mcbond_it 0.663 r_chiral_restr 0.086 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 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 1562 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement Coot model building PHASER phasing Aimless data scaling XDS data reduction