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Rubrerythrin from B. pseudomallei: manganese-bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 295 0.138 M Li2SO4, 0.92 M BTP, pH 8, 22.08% PEG 3350, 0.8 mM MnCl2
Crystal Properties Matthews coefficient Solvent content 2.42 49.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 201.874 α = 90 b = 201.874 β = 90 c = 69.025 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 2022-06-22 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 1.58 29.14 93.7 0.092 0.115 0.069 0.998 9.5 5.2 108953
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 1.58 1.692 59.3 0.833 1.161 0.807 0.457 3.1
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 FREE R-VALUE 1.58 29.14 108953 5467 93.7 0.149 0.1477 0.1478 0.1755 0.1755 19.178
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] 0.003 0.001 0.003 -0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.938 r_dihedral_angle_3_deg 14.738 r_lrange_it 6.82 r_dihedral_angle_2_deg 6.713 r_lrange_other 6.578 r_scangle_it 5.823 r_scangle_other 5.822 r_dihedral_angle_1_deg 4.57 r_scbond_it 3.629 r_scbond_other 3.628
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.938 r_dihedral_angle_3_deg 14.738 r_lrange_it 6.82 r_dihedral_angle_2_deg 6.713 r_lrange_other 6.578 r_scangle_it 5.823 r_scangle_other 5.822 r_dihedral_angle_1_deg 4.57 r_scbond_it 3.629 r_scbond_other 3.628 r_mcangle_other 2.536 r_mcangle_it 2.533 r_mcbond_it 1.824 r_mcbond_other 1.82 r_angle_refined_deg 1.529 r_angle_other_deg 0.548 r_symmetry_nbd_refined 0.38 r_nbd_other 0.343 r_nbd_refined 0.232 r_xyhbond_nbd_refined 0.189 r_nbtor_refined 0.188 r_symmetry_nbd_other 0.174 r_symmetry_xyhbond_nbd_refined 0.123 r_chiral_restr 0.083 r_symmetry_nbtor_other 0.07 r_bond_refined_d 0.009 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 6443 Nucleic Acid Atoms Solvent Atoms 874 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling MOLREP phasing