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Crystal structure of OxdB E85A mutant (form I)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A15
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 30 % (w/v) polyethylene glycol 4,000, 0.1 M Tris pH8.5, and 0.2 M magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.35 47.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.306 α = 90 b = 63.774 β = 94.22 c = 59.246 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 2018-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90000 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.55 36.06 99.29 0.03188 0.03798 0.02042 0.999 19.1 3.4 51535 28.12
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.61 97.64 0.5184 0.6151 0.3276 0.733 2.06 3.5
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 3a15 1.55 36.06 46369 5167 99.29 0.17455 0.17186 0.1856 0.19896 0.2111 RANDOM 31.101
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] -0.83 0.26 -0.66 1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.02 r_dihedral_angle_3_deg 13.236 r_dihedral_angle_4_deg 10.717 r_dihedral_angle_1_deg 7.346 r_long_range_B_refined 4.076 r_long_range_B_other 4.052 r_scangle_other 2.773 r_mcangle_it 1.946 r_mcangle_other 1.945 r_scbond_other 1.912
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.02 r_dihedral_angle_3_deg 13.236 r_dihedral_angle_4_deg 10.717 r_dihedral_angle_1_deg 7.346 r_long_range_B_refined 4.076 r_long_range_B_other 4.052 r_scangle_other 2.773 r_mcangle_it 1.946 r_mcangle_other 1.945 r_scbond_other 1.912 r_scbond_it 1.911 r_angle_refined_deg 1.844 r_angle_other_deg 1.519 r_mcbond_other 1.407 r_mcbond_it 1.406 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.013 r_gen_planes_other 0.009 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 2657 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement Coot model building MOLREP phasing Aimless data scaling XDS data reduction