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Crystal structure of a peptide deformylase from Burkholderia multivorans in complex with actinonin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HGW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 289 MCSG1 F4 (272591f4): 40% (v/v) PEG 400, 200 mM Magnesium chloride, 100 mM Sodium citrate:citric acid pH 5.5, 3 mM actinonin; direct cryo; puck kur4-4
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.12 α = 90 b = 70.54 β = 90 c = 140.51 γ = 90
Symmetry Space Group I 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 CCD RAYONIX MX-300 2016-06-22 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 1.85 39.019 99.9 0.047 0.051 0.999 22.71 17066 -3 28.83
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 1.85 1.9 99.9 0.485 0.522 0.951 3.88
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 5hgw 1.85 39.019 1.35 17057 1681 99.87 0.1689 0.1651 0.1678 0.2032 0.2057 40.4415
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 12.245 f_angle_d 0.997 f_chiral_restr 0.069 f_bond_d 0.01 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1249 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 28
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling MOLREP phasing PDB_EXTRACT data extraction Coot model building XDS data scaling