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Crystal structure of MnmA D100C mutant from Streptococcus pneumoniae with [4Fe-4S] cluster in complex with formate
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 7 293 ANAEROBY (<1.5 ppm O2)
3.5M Sodium formate 0.1M Bis-tris propane pH 7.0
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.452 α = 90 b = 93.452 β = 90 c = 159.02 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 2023-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.980 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 1.92 19.81 94.8 0.2149 0.2204 0.0485 0.998 10.73 20.45 39900
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) 1.922 2.133 75.8 1.4187 1.4561 0.3247 0.888 2.12 19.98 1995
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 1.92 19.81 1.35 39890 2012 64.61 0.1636 0.1622 0.1629 0.1896 0.1896 35.61
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 17.0925 f_angle_d 0.8312 f_chiral_restr 0.0487 f_bond_d 0.0064 f_plane_restr 0.0057
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2894 Nucleic Acid Atoms Solvent Atoms 414 Heterogen Atoms 63
Software Software Software Name Purpose PHENIX refinement autoPROC data processing XDS data reduction STARANISO data scaling PHASER phasing Coot model building