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Malic semialdehyde dehydrogenase (MSA-DH) from Acinetobacter baumannii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.3 298 Jena Bioscience Pi-PEG screen condition G8:
34.3 % (w/v) PEG 550 monomethyl ether,
2.9 % (w/v) PEG 300,
50 mM HEPES/NaOH pH 7.3
Additive: 7 mM D-malate
Crystal Properties Matthews coefficient Solvent content 3.85 68.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.966 α = 90 b = 194.288 β = 90 c = 454.336 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER2 X 16M 2023-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.03322 PETRA III, DESY P11
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 2.59 19.8 99.5 0.15 0.156 0.044 0.998 10.7 12.5 316761
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 2.59 2.73 99.8 1.256 1.311 0.372 0.887 12.2
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 2.59 19.8 1.34 316278 15935 99.58 0.1812 0.1798 0.1798 0.2074 0.2074
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 16.028 f_angle_d 0.459 f_chiral_restr 0.041 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 43866 Nucleic Acid Atoms Solvent Atoms 859 Heterogen Atoms 135
Software Software Software Name Purpose autoPROC data processing XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement Coot model building