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Crystal structure of the hemophore HasA from Pseudomonas protegens Pf-5 capturing Fe-tetraphenylporphyrin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model SwissModel
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 100 mM Tris-HCl (pH 7.0), 1.0 M Potassium sodium tartrate, 200 mM Lithium sulfate
Crystal Properties Matthews coefficient Solvent content 2.32 47.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.561 α = 90 b = 158.717 β = 97.58 c = 33.534 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 4M 2019-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.000 SPring-8 BL26B1
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 1.45 39.68 95.5 0.076 0.082 0.998 16.08 6.54 59034
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 1.45 1.53 87.7 0.374 0.414 0.907 4.38
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 1.45 39.68 55595 3011 95.57 0.12065 0.11899 0.1258 0.15178 0.1577 RANDOM 12.825
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] -2.44 -1.43 4.4 -1.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.428 r_dihedral_angle_4_deg 27.189 r_dihedral_angle_3_deg 11.478 r_dihedral_angle_1_deg 6.033 r_long_range_B_refined 2.089 r_long_range_B_other 1.947 r_scangle_other 1.546 r_angle_refined_deg 1.54 r_angle_other_deg 1.484 r_mcangle_it 1.331
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.428 r_dihedral_angle_4_deg 27.189 r_dihedral_angle_3_deg 11.478 r_dihedral_angle_1_deg 6.033 r_long_range_B_refined 2.089 r_long_range_B_other 1.947 r_scangle_other 1.546 r_angle_refined_deg 1.54 r_angle_other_deg 1.484 r_mcangle_it 1.331 r_mcangle_other 1.331 r_scbond_it 1.33 r_scbond_other 1.329 r_mcbond_it 1.068 r_mcbond_other 1.06 r_rigid_bond_restr 0.966 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2624 Nucleic Acid Atoms Solvent Atoms 309 Heterogen Atoms 144
Software Software Software Name Purpose XDS data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing