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Rubrerythrin from B. pseudomallei: apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DI0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 296 0.5 M lithium sulfate, 0.1 M bis-tris propane, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.48 50.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 202.373 α = 90 b = 202.373 β = 90 c = 70.329 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 2022-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.92010 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 1.85 29.21 99.4 0.101 0.138 0.093 0.993 6.5 3.6 90867
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 1.85 1.88 0.676 0.934 0.643 0.608 3.3
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 1.852 28.748 90850 4443 99.406 0.152 0.1497 0.1507 0.1875 0.1899 24.497
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] -0.613 -0.307 -0.613 1.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.94 r_dihedral_angle_3_deg 14.752 r_dihedral_angle_2_deg 6.613 r_lrange_it 5.952 r_lrange_other 5.686 r_dihedral_angle_1_deg 4.903 r_scangle_it 4.656 r_scangle_other 4.655 r_mcangle_other 3.111 r_mcangle_it 3.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.94 r_dihedral_angle_3_deg 14.752 r_dihedral_angle_2_deg 6.613 r_lrange_it 5.952 r_lrange_other 5.686 r_dihedral_angle_1_deg 4.903 r_scangle_it 4.656 r_scangle_other 4.655 r_mcangle_other 3.111 r_mcangle_it 3.109 r_scbond_it 3.034 r_scbond_other 3.031 r_mcbond_it 2.209 r_mcbond_other 2.207 r_angle_refined_deg 1.416 r_angle_other_deg 0.524 r_nbd_refined 0.233 r_nbtor_refined 0.185 r_symmetry_nbd_other 0.173 r_symmetry_nbd_refined 0.169 r_xyhbond_nbd_refined 0.161 r_symmetry_xyhbond_nbd_refined 0.132 r_nbd_other 0.13 r_chiral_restr 0.076 r_symmetry_xyhbond_nbd_other 0.073 r_symmetry_nbtor_other 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6468 Nucleic Acid Atoms Solvent Atoms 936 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement Aimless data scaling Coot model building MOLREP phasing