☰ Navigation Tabs
Crystal structure of a peptide deformylase from Burkholderia ambifaria
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NT8 PDB entry 4nt8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290 Rigaku ReagentsJCSG+ screen E2: 200mM ammonium sulphate, 200mM NaCl, 100mM Na-cacodylate/HCl pH 6.5; BuamA.00078.a.B1.PS02512 at 17.5 mg/ml, tray 267395 e2, puck pud2-3
Crystal Properties Matthews coefficient Solvent content 3.02 59.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.69 α = 90 b = 121.35 β = 90 c = 71.29 γ = 90
Symmetry Space Group C 2 2 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 RIGAKU SATURN 944+ 2015-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.6 50 99.9 0.054 0.056 29.53 11.1 66910 66817 -3 12.33
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.64 99.1 0.548 0.587 4.02 7.75
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 4nt8 1.6 50 1.34 66804 2107 99.84 0.1544 0.1536 0.1784 0.1538 Random selection 17.5828
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 14.438 f_angle_d 1.18 f_chiral_restr 0.08 f_bond_d 0.012 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2738 Nucleic Acid Atoms Solvent Atoms 586 Heterogen Atoms 58
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PHASER phasing PDB_EXTRACT data extraction Coot model building