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OppA from E. coli in complex with GSisoK
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TCF Crystal structure of E. coli OppA complexed with endogenous ligands
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 15% Ethanol, 40% Pentaerythritol propoxylate
Crystal Properties Matthews coefficient Solvent content 2.61 52.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.99 α = 90 b = 200.69 β = 95.73 c = 103.38 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 EIGER X 16M 2025-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.0597 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.5 30 95.8 0.119 7.5 3.1 80198
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 99.6 0.688 2 3.2
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 MOLECULAR REPLACEMENT THROUGHOUT 2.5 30 76162 4008 95.73 0.23142 0.22936 0.2407 0.2593 0.2679 RANDOM 34.5
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] 5.32 0.08 -2.18 -3.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.495 r_dihedral_angle_3_deg 15.488 r_dihedral_angle_4_deg 14.81 r_dihedral_angle_1_deg 5.735 r_long_range_B_refined 1.476 r_long_range_B_other 1.474 r_angle_refined_deg 1.193 r_angle_other_deg 1.091 r_mcangle_it 0.989 r_mcangle_other 0.989
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.495 r_dihedral_angle_3_deg 15.488 r_dihedral_angle_4_deg 14.81 r_dihedral_angle_1_deg 5.735 r_long_range_B_refined 1.476 r_long_range_B_other 1.474 r_angle_refined_deg 1.193 r_angle_other_deg 1.091 r_mcangle_it 0.989 r_mcangle_other 0.989 r_scangle_other 0.859 r_mcbond_it 0.686 r_mcbond_other 0.685 r_scbond_other 0.591 r_scbond_it 0.59 r_rigid_bond_restr 0.23 r_chiral_restr 0.038 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.002 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16492 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing