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Crystal Structure of HasAp Capturing Iron Tetra(4-pyridyl)porphyrin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ELL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 100mM Tris-HCl (pH 8.5), 1260mM Ammonium sulfate, 200mM Lithium sulfate
Crystal Properties Matthews coefficient Solvent content 2.33 47.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.318 α = 99.17 b = 43.981 β = 93.9 c = 130.116 γ = 92.87
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 2020-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.000 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2 43.37 97.2 0.086 0.109 0.996 6.29 2.596 44520 24.745
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.06 95 0.342 0.429 0.927 2.3 2.665
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 3ELL 2 43.37 42292 2227 97.2 0.2307 0.2292 0.2346 0.2604 0.2669 RANDOM 17.047
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] -0.18 -0.57 -0.09 1.49 -1.63 -0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.693 r_dihedral_angle_4_deg 21.853 r_dihedral_angle_3_deg 12.996 r_dihedral_angle_1_deg 6.31 r_angle_other_deg 1.663 r_angle_refined_deg 1.573 r_chiral_restr 0.069 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.693 r_dihedral_angle_4_deg 21.853 r_dihedral_angle_3_deg 12.996 r_dihedral_angle_1_deg 6.31 r_angle_other_deg 1.663 r_angle_refined_deg 1.573 r_chiral_restr 0.069 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5304 Nucleic Acid Atoms Solvent Atoms 624 Heterogen Atoms 214
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing