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Crystal Structure of Hemophore HphA from A. baumannii with Cobalt Phthalocyanine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7RED
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 1.26 M ammonium sulfate, 0.1 M HEPES-NaOH pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.63 53.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.264 α = 90 b = 62.957 β = 90 c = 70.483 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS3 X 6M 2023-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.000 SPring-8 BL45XU
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 1.41 47 100 0.187 0.196 0.059 0.993 9.3 10 49845 10.09
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 1.41 1.43 100 1.61 1.716 0.584 0.586 8.2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.41 46.998 49786 2502 99.946 0.131 0.1289 0.1378 0.1597 0.1647 15.389
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] 0.313 -0.836 0.523
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.214 r_lrange_it 11.518 r_lrange_other 10.078 r_dihedral_angle_3_deg 9.418 r_scangle_it 7.198 r_dihedral_angle_1_deg 6.925 r_scangle_other 6.803 r_scbond_it 5.133 r_mcangle_other 4.92 r_mcangle_it 4.909
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.214 r_lrange_it 11.518 r_lrange_other 10.078 r_dihedral_angle_3_deg 9.418 r_scangle_it 7.198 r_dihedral_angle_1_deg 6.925 r_scangle_other 6.803 r_scbond_it 5.133 r_mcangle_other 4.92 r_mcangle_it 4.909 r_scbond_other 4.779 r_rigid_bond_restr 3.959 r_mcbond_it 3.526 r_mcbond_other 3.508 r_angle_refined_deg 1.637 r_angle_other_deg 0.605 r_symmetry_nbd_other 0.197 r_nbd_refined 0.194 r_nbtor_refined 0.183 r_symmetry_xyhbond_nbd_refined 0.171 r_nbd_other 0.156 r_symmetry_nbd_refined 0.143 r_xyhbond_nbd_refined 0.126 r_chiral_restr 0.098 r_symmetry_nbtor_other 0.089 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1685 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing