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Crystal structure of the T19D mutant of the de novo diheme binding 4D2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7AH0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Crystallisation buffer: 2.1 M DL-malic acid,
Purification buffer: 20 mM CHES, 100mM KCl, pH 8.6
Crystal Properties Matthews coefficient Solvent content 3.12 60.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.093 α = 90 b = 81.093 β = 90 c = 58.585 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 193 PIXEL DECTRIS EIGER2 X 16M 2021-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.1 40.58 100 0.102 0.105 15.4 21.2 8376
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 100 0.367 0.376 3.8 21.4
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 2.1 40.55 7531 840 99.99 0.20292 0.1995 0.2043 0.23259 0.2272 RANDOM 44.276
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] 0.07 0.03 0.07 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.349 r_dihedral_angle_4_deg 28.746 r_dihedral_angle_3_deg 17.389 r_long_range_B_other 8.016 r_long_range_B_refined 8 r_scangle_other 6.248 r_dihedral_angle_1_deg 5.12 r_mcangle_it 4.884 r_mcangle_other 4.884 r_scbond_it 4.161
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.349 r_dihedral_angle_4_deg 28.746 r_dihedral_angle_3_deg 17.389 r_long_range_B_other 8.016 r_long_range_B_refined 8 r_scangle_other 6.248 r_dihedral_angle_1_deg 5.12 r_mcangle_it 4.884 r_mcangle_other 4.884 r_scbond_it 4.161 r_scbond_other 4.133 r_mcbond_it 2.978 r_mcbond_other 2.97 r_angle_other_deg 2.578 r_angle_refined_deg 2.561 r_chiral_restr 0.238 r_gen_planes_other 0.067 r_bond_other_d 0.034 r_gen_planes_refined 0.029 r_bond_refined_d 0.022 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 837 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement xia2 data scaling DIALS data reduction MOLREP phasing