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Crystal structure of the diheme 4D2 (mutant T19D) with bound Fe(III) mesoporphyrin IX
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8CCR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 2.1M DL-Malic acid, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.95 58.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.187 α = 90 b = 81.187 β = 90 c = 58.817 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 XE 16M 2023-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.95373 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.98 45.11 100 0.082 0.988 11.2 85.6 10079
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 1.98 2.01 100 0.402
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 1.98 45.11 9552 526 99.99 0.19818 0.1954 0.1973 0.25405 0.2577 RANDOM 58.674
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] 1.71 1.71 -3.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.31 r_long_range_B_refined 14.268 r_scbond_it 8.99 r_mcangle_it 8.671 r_mcbond_it 6.671 r_dihedral_angle_1_deg 5.447 r_dihedral_angle_2_deg 5.127 r_angle_refined_deg 2.498 r_chiral_restr 0.119 r_bond_refined_d 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.31 r_long_range_B_refined 14.268 r_scbond_it 8.99 r_mcangle_it 8.671 r_mcbond_it 6.671 r_dihedral_angle_1_deg 5.447 r_dihedral_angle_2_deg 5.127 r_angle_refined_deg 2.498 r_chiral_restr 0.119 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 828 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement xia2.multiplex data reduction xia2.multiplex data scaling MOLREP phasing