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OXA-58-NA-1-157 10 min complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OH0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 0.2 M sodium acetate, 0.1 M Tris-HCl pH 8.5, 30% PEG4000
Crystal Properties Matthews coefficient Solvent content 1.87 34.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.01 α = 90 b = 65.771 β = 91.19 c = 193.101 γ = 90
Symmetry Space Group P 1 21 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 EIGER2 XE 16M 2024-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.94 54.41 91.3 0.205 0.08 0.981 5.3 6.5 62529
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 1.98 0.64 0.558 1.2
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 FOURIER SYNTHESIS THROUGHOUT 1.94 54.41 59268 3010 91.11 0.21995 0.21846 0.2236 0.24871 0.2548 RANDOM 29.554
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] -2.62 0.59 3.31 -0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.705 r_dihedral_angle_1_deg 5.87 r_dihedral_angle_2_deg 3.219 r_long_range_B_refined 3.089 r_long_range_B_other 3.063 r_scangle_other 1.847 r_mcangle_it 1.806 r_mcangle_other 1.806 r_angle_refined_deg 1.044 r_scbond_it 1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.705 r_dihedral_angle_1_deg 5.87 r_dihedral_angle_2_deg 3.219 r_long_range_B_refined 3.089 r_long_range_B_other 3.063 r_scangle_other 1.847 r_mcangle_it 1.806 r_mcangle_other 1.806 r_angle_refined_deg 1.044 r_scbond_it 1.04 r_scbond_other 1.04 r_mcbond_it 1.03 r_mcbond_other 1.03 r_angle_other_deg 0.366 r_chiral_restr 0.048 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 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 7644 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms 110
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling MOLREP phasing