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OleP mutant S240Y in complex with 6DEB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MNS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 Sodium Formate, 4.4 M
Crystal Properties Matthews coefficient Solvent content 3.13 60.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 248.624 α = 90 b = 110.355 β = 129.63 c = 160.046 γ = 90
Symmetry Space Group C 1 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 2020-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.000 ELETTRA 11.2C
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 2.5 51.34 99.2 0.992 5.59 4 225386
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 2.5 2.65 99.1 0.1
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 5mns 2.7 51.34 87164 4388 99.9 0.20721 0.20414 0.206 0.26804 0.2682 RANDOM 65.582
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] -1.27 -0.23 1.84 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.317 r_dihedral_angle_3_deg 19.137 r_dihedral_angle_4_deg 18.388 r_long_range_B_refined 7.741 r_long_range_B_other 7.74 r_dihedral_angle_1_deg 6.807 r_mcangle_it 5.425 r_mcangle_other 5.424 r_scangle_other 5.036 r_mcbond_it 3.348
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.317 r_dihedral_angle_3_deg 19.137 r_dihedral_angle_4_deg 18.388 r_long_range_B_refined 7.741 r_long_range_B_other 7.74 r_dihedral_angle_1_deg 6.807 r_mcangle_it 5.425 r_mcangle_other 5.424 r_scangle_other 5.036 r_mcbond_it 3.348 r_mcbond_other 3.348 r_scbond_it 3.028 r_scbond_other 3.026 r_angle_refined_deg 1.524 r_angle_other_deg 1.235 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 r_bond_other_d 0.002 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 18627 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 438
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing