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Crystal structure of the enoyl reductase domain of DfnA from Bacillus amyloliquefaciens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z6I PDB ENTRY 2Z6I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 15 % PEG3350, 0.1 M SODIUM MALONATE, BIS TRIS PH 6.0
Crystal Properties Matthews coefficient Solvent content 2.74 55.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.85 α = 90 b = 94 β = 90 c = 144.53 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 PILATUS 2M 2013-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.25 47 99.9 0.08 18.3 6.6 49619 1.68
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.38 99.8 1.23 1.68 6.5
Refinement Statistics Diffraction ID Structure Solution 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 2Z6I 2.3 47 1.99 49619 2504 99.96 0.2053 0.204 0.2079 0.2309 0.234
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 15.176 f_angle_d 0.84 f_chiral_restr 0.031 f_bond_d 0.004 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6797 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 62
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing