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Crystal Structure of dihydrodipicolinate reductase from Acinetobacter baumannii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YWJ pdb entry 4ywj as per Morda
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.8 287 RigakuReagents JCSG+ screen, condition a2, optimized: 100mM sodium citrate tribasic / citric acid pH 5.8, 22% (w/V) PEG 3000: AcbaC.00189.a.B1.PW38917 at 19mg/ml + 4mM NAD. Tray 324181 c6: cryo: 20% EG with NAD: puck ybo0-10.
Crystal Properties Matthews coefficient Solvent content 2.68 54.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.8 α = 90 b = 79.8 β = 90 c = 519.13 γ = 120
Symmetry Space Group P 31 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 CCD RAYONIX MX-300 Beryllium Lenses 2022-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.65 50 99.1 0.072 0.079 0.998 13.64 5.5 57256 71.999
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.72 98.8 0.646 0.712 0.899 2.8 5.655
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE pdb entry 4ywj as per Morda 2.65 41.51 1.35 57163 1975 99.23 0.2087 0.2077 0.2077 0.2347 0.2346 0 86.74
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 12.8306 f_angle_d 0.658 f_chiral_restr 0.0467 f_plane_restr 0.0053 f_bond_d 0.0044
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11127 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 78
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction MoRDa phasing PHENIX model building Coot model building