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Crystal structure of a novel fatty acid decarboxylase from Rothia nasimurium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IZO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 25 % (w/v) PEG3500, 15% (w/v) 2-Methil-2,4-pentanediol, 0.1 M Imidazole (pH 6.5) and 0.2 M lithium sulfate
Crystal Properties Matthews coefficient Solvent content 2.44 49.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.545 α = 90 b = 203.38 β = 90 c = 316.351 γ = 90
Symmetry Space Group F 2 2 2
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 2020-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS SIRUS BEAMLINE MANACA 1.4586 LNLS SIRUS MANACA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.75 49.02 99.8 0.35 0.98 5.9 5.9 24500 74.46
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.92 99.7 0.5 0.98
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1IZO 2.75 48.41 1.33 24494 1226 99.84 0.2301 0.228 0.2281 0.2692 0.2692 78.51
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 10.4189 f_angle_d 0.8311 f_chiral_restr 0.041 f_plane_restr 0.0134 f_bond_d 0.0048
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6514 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 182
Software Software Software Name Purpose PHASER phasing PHENIX refinement XDS data reduction XSCALE data scaling