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Crystal structure of a peptide deformylase from Burkholderia xenovorans in complex with actinonin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KOB PDB entry 5KOB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 1:1 22 mg/mL BuxeA.00078.a.B1.PS37823 / Rigaku reagents Morpheus A8 (0.03 M magnesium chloride, 0.03 M calcium chloride, 0.1 M HEPES/MOPS, pH 7.5, 12.5% MPD, 12.5% PEG1000, 12.5% PEG3350), crystal id: wda5-2 270123a8
Crystal Properties Matthews coefficient Solvent content 2.39 48.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.11 α = 90 b = 90.33 β = 90 c = 140.21 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 CCD MARMOSAIC 225 mm CCD 2016-02-24 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 1.95 48.536 99.8 0.04 0.044 1 23.88 6.138 59117 -3 34.02
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 1.95 2 100 0.53 0.578 0.944 3.79 6.205
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 PDB entry 5KOB 1.95 48.536 1.35 59092 1926 99.76 0.1625 0.1615 0.1637 0.1918 0.1932 47.11
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 13.498 f_angle_d 1.062 f_chiral_restr 0.047 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4934 Nucleic Acid Atoms Solvent Atoms 348 Heterogen Atoms 115
Software Software Software Name Purpose XSCALE data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing