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Crystal structure of MnmA D100C mutant from Streptococcus pneumoniae with [4Fe-5Se] cluster
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HMA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 ANAEROBY (<1.5 ppm O2)
3.5M Sodium formate 0.1M Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 4.87 74.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.272 α = 90 b = 94.272 β = 90 c = 158.986 γ = 120
Symmetry Space Group P 32 2 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 9M 2024-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.97487 SOLEIL PROXIMA 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 2.37 19.85 80.7 0.257 0.261 0.047 0.997 12.2 30.8 27317 39.82
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 2.37 2.58 2.321 2.362 0.436 0.8428 1.556
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.37 19.85 1.36 27312 1364 80.69 0.1701 0.1686 0.1694 0.1986 0.1971 47.59
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 19.472 f_angle_d 0.9174 f_chiral_restr 0.0482 f_bond_d 0.0076 f_plane_restr 0.0069
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2854 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 75
Software Software Software Name Purpose PHENIX refinement autoPROC data processing XDS data reduction STARANISO data scaling PHASER phasing Coot model building