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OleP mutant E89Y 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, 4.4M
Crystal Properties Matthews coefficient Solvent content 3.15 60.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 248.135 α = 90 b = 111.117 β = 129.67 c = 160.543 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 2019-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 0.9788 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.44 48.07 98.2 0.048 0.99 13.55 3 241832
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.44 2.59 96.7 0.598 0.747 1.81
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 2.44 48.07 117365 5991 99.05 0.18988 0.18714 0.2001 0.24333 0.2477 RANDOM 60.212
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] -2.82 -1.11 2.45 0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.999 r_dihedral_angle_4_deg 18.546 r_dihedral_angle_3_deg 18.249 r_long_range_B_refined 9.129 r_long_range_B_other 9.129 r_scangle_other 6.866 r_dihedral_angle_1_deg 6.794 r_mcangle_it 6.676 r_mcangle_other 6.675 r_scbond_it 4.622
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.999 r_dihedral_angle_4_deg 18.546 r_dihedral_angle_3_deg 18.249 r_long_range_B_refined 9.129 r_long_range_B_other 9.129 r_scangle_other 6.866 r_dihedral_angle_1_deg 6.794 r_mcangle_it 6.676 r_mcangle_other 6.675 r_scbond_it 4.622 r_mcbond_it 4.605 r_mcbond_other 4.604 r_scbond_other 4.598 r_angle_refined_deg 1.555 r_angle_other_deg 1.213 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 r_bond_other_d 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 18485 Nucleic Acid Atoms Solvent Atoms 375 Heterogen Atoms 603
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing