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Rubrerythrin from B. pseudomallei: iron-bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other 8FUH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6.75 273 0.15 M lithium sulfate
30% PEG 3350
0.1 M BTP pH 6.75
1 mM iron chloride
Crystal Properties Matthews coefficient Solvent content 2.45 49.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 202.17 α = 90 b = 202.17 β = 90 c = 69.825 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 100 PIXEL DECTRIS EIGER X 16M 2022-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.97934 NSLS-II 17-ID-2
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 1.93 29.9 92.4 0.23 0.241 0.073 0.995 8.9 10.8 61079 2 13.99
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 2.07 61.4 1.898 0.607 0.597 1.5 10.7
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.93 29.9 61079 2998 92.4 0.163 0.161 0.1608 0.209 0.2086 RANDOM 24.663
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] -0.013 -0.006 -0.013 0.042
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.485 r_dihedral_angle_3_deg 15.019 r_lrange_it 6.688 r_lrange_other 6.441 r_dihedral_angle_2_deg 6.339 r_dihedral_angle_1_deg 5.002 r_scangle_it 4.912 r_scangle_other 4.912 r_mcangle_other 3.147 r_mcangle_it 3.146
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.485 r_dihedral_angle_3_deg 15.019 r_lrange_it 6.688 r_lrange_other 6.441 r_dihedral_angle_2_deg 6.339 r_dihedral_angle_1_deg 5.002 r_scangle_it 4.912 r_scangle_other 4.912 r_mcangle_other 3.147 r_mcangle_it 3.146 r_scbond_it 3.08 r_scbond_other 3.08 r_mcbond_it 2.066 r_mcbond_other 2.066 r_angle_refined_deg 1.38 r_angle_other_deg 0.479 r_nbd_refined 0.23 r_nbd_other 0.21 r_symmetry_nbd_refined 0.208 r_xyhbond_nbd_refined 0.206 r_nbtor_refined 0.188 r_symmetry_nbd_other 0.179 r_symmetry_xyhbond_nbd_refined 0.143 r_metal_ion_refined 0.1 r_symmetry_nbtor_other 0.072 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6464 Nucleic Acid Atoms Solvent Atoms 800 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling MOLREP phasing