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Crystal structure of MnmA from Streptococcus pneumoniae in complex with ATP
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 6.5 293 2M ammonium sulfate, 5% w/v PEG 400, 0.1M MES pH 6.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.992 α = 90 b = 94.992 β = 90 c = 159.095 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 16M 2023-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.978 SOLEIL PROXIMA 1
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 1.9 19.912 95.4 0.1301 0.1335 0.0295 0.999 17.48 20.42 44516
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) 1.902 2.122 73.3 2.1011 2.1589 0.4917 0.574 1.66 19.08 2226
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 1.9 19.91 1.35 44513 2243 67.66 0.1724 0.171 0.171 0.1976 0.1977 46.34
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 21.2663 f_angle_d 0.8679 f_chiral_restr 0.0488 f_plane_restr 0.0072 f_bond_d 0.0062
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2830 Nucleic Acid Atoms Solvent Atoms 282 Heterogen Atoms 115
Software Software Software Name Purpose autoPROC data processing XDS data reduction STARANISO data scaling PHENIX refinement PHASER phasing Coot model building